edu) Date: Mon May 28 2007 - 10:33:29 CDT Next message: Gianluca Interlandi: "Re: Protein in/out of box" Previous message: Peter Freddolino: "Re: constraints on zinc ions" In reply to: Monika Sharma: "Protein in/out of box" Next in. how to output more significant figures in a file for energies and forces? Next message: Gianluca Interlandi: "Re: accuracy of measurement"Locking up the spike protein to prevent infection. washington. I want to simulate a protein > attached to mannose. washington. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. From: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. washington. washington. I needed to install the 'patch' program. Re: Yet another NAMD speed concerns. washington. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). washington. > On Fri, 9 Feb 2007, Gianluca Interlandi wrote: > > > Dear Marcos, > > > > Thanks a lot for your answer and for offering me your help. 1002/prot. (2010) The catch bond mechanism between von Willebrand factor and platelet surface receptors investigated by molecular dynamics simulations. washington. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. uiuc. washington. washington. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. com) Date: Sat Jul 04 2015 - 10:49:22 CDT Next message: Gianluca Interlandi: "multicore vs ibverbs" Previous message: Josh Vermaas: "Re: extra bonds" Maybe in reply to: Mitchell Gleed: "Re: replica exchange and GPU acceleration" Next in. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallmargin errors. washington. 7 released" Messages sorted by: [ attachment ] Hi all, I pushed 2. It's > slightly faster but still not that much faster than running on 16 CPU cores. edu) Date: Tue Sep 15 2020 - 20:34:44 CDT Next message: Kodituwakku,Dimuthu Nirmani: "Re: Post processing NAMD trajectory" Previous message: Victor Zhao: "Re: Re: AMBER input and REST2 leads to crash" Next in thread:. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. From: Mitchell Gleed (aliigleed16_at_gmail. AMBER does, and so does GROMACS. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. edu> wrote: > Hi Fatemeh, > > Thanks for replying. Katrina T. You should simulate it in explicit water (or try one of the implicitNext in thread: Gianluca Interlandi: "Re: accuracy of measurement" Reply: Gianluca Interlandi: "Re: accuracy of measurement" Messages sorted by: [ attachment ] hi namd users. Sokurenko 1 , *. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. I doubt that there is a way to haveReply: Gianluca Interlandi: "Re: NAMD timestep and numsteps" Messages sorted by: [ attachment ] Hi NAMD users, I was running a simulation using NAMD with timestep 5 fs and numsteps 5000. washington. edu) Date: Thu Nov 02 2006 - 15:40:40 CST Next message: Gianluca Interlandi: "Re: SMD on center of mass" Previous message: Ugur Akgun: "ABF on a single molecule" In reply to: Gianluca Interlandi: "Re: external force" Next in. rtf" and "par_all36_prot. Hemostasis in vertebrates involves both a. edu) Date: Mon Apr 11 2011 - 14:41:28 CDT Next message: Axel Kohlmeyer: "Re: Help building a desktop for namd" Previous message: Buddhadev Maiti: "(no subject)" In reply to: Axel Kohlmeyer: "Re: Help building a desktop for namd" Next in. From: Gianluca Interlandi (gianluca_at_u. uiuc. edu> > wrote: > Roy, > > I think that you are confusing two things. > You could build a PC with the Asus p5Q Pro Motherboard, Intel Quadcore Q8200 > and two GTX 285 cards for under 900$ (plus the cost of the usual PC > components). (2010) The catch bond mechanism between von Willebrand factor and platelets investigated by molecular dynamics simulations. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. Biochemistry. washington. PMID: 37700555; DOI: 10. uiuc. On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi < gianluca_at_u. 9. MyOn Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi < gianluca_at_u. 6 version, although I am not running the cluster at full load yet. washington. washington. edu> wrote: >> if you want to go low risk and don't have much experience with GPU, then >> probably the best deal you can currently get for running. edu) Date: Wed Sep 23 2015 - 13:37:27 CDT Next message: Gianluca Interlandi: "SSD vs SSHD vs mechanical" Previous message: Mayne, Christopher G: "Re: FFTK Bond optimization" In reply to: Gianluca Interlandi: "SSD vs SSHD vs mechanical" Next in thread: Gianluca Interlandi: "Re:. Comparative controls consisted of FocH (high affinity with and. edu> Cc: <namd-l_at_ks. 6 ns/day for a 100k atom system with roughly those same parameters (and. " Previous message: Gianluca Interlandi: "multicore vs ibverbs" Messages sorted by: [ attachment ] Dear NAMD list, I am a bit. If I > want to use all 6 CUDA devices in a node, how many processes is it > recommended to spawn?> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. > > Forget about creating a pdb file. washington. edu Search for more. washington. edu Phone: (206)685-4435 Office: Foege N430 E Gianluca Interlandi I am interested in. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. Facilities. I doubt that there is a way to have NAMD output theReply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] have you tried the multicore build? I wonder if the prebuilt smp one is just not working for you. washington. Research Assistant Professor (Independent Lab) e-mail: gianluca@u. Sarah Keller Professor. washington. 7 released" Messages sorted by: [ attachment ] Thank you very much! It seems to be up to 40% faster than the 2. Previous message: Gianluca Interlandi: "NAMD 2. Gianluca Interlandi [email protected] orcid. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. edu) Date: Thu Apr 07 2011 - 13:57:41 CDT Next message: Axel Kohlmeyer: "Re: Abe versus Lincoln" Previous message: Gianluca Interlandi: "Re: Abe versus Lincoln" In reply to: Axel Kohlmeyer: "Re: Abe versus Lincoln"From: Gianluca Interlandi (gianluca_at_u. Previous message: Gianluca Interlandi: "Re: tools for Charmm" In reply to: Gianluca Interlandi: "Re: Charmm" Messages sorted by: [ attachment ] On 02/20/2014 01:10 PM, Gianluca Interlandi wrote: > I usually use the CHARMM program itself to generate a CHARMM PSF file. washington. edu] Sent: Friday, June 17, 2016 2:29 PM To: Richard Wood Cc: John Stone; vmd-l_at_ks. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. edu> > wrote: > are other people also using those GPUs? > >Previous message: Gianluca Interlandi: "Conversion for forces" In reply to: Gianluca Interlandi: "Conversion for forces" Next in thread: Gianluca Interlandi: "SMD and restart" Reply: Gianluca Interlandi: "SMD and restart" Messages sorted by: [ attachment ] kcal/mol/A^2 is actually units for a force constant (for a spring for. washington. I empolyed PBC condition with wraping water and wraping all options on. From: Gianluca Interlandi (gianluca_at_u. You can specify the nice priority in a nodelist file, for example: group main ++nice 19 host machine1 ++nice 20 host machine2 ++nice 21 host machine3> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. washington. 25050 [PMC free article] [Google Scholar] EDUCATION<br><br>2012 November: WHR Seminar: Seminar about Hotel Revenue, web e social Marketing at Hotel Le Le Capannelle, Roma, Italy (Nov. edu) Date: Fri May 04 2007 - 17:53:42 CDT Next message: Lechuga, Javier: "Simulating air with NAMD" Previous message: Gianluca Interlandi: "Re: query about wrapped coordinates" Maybe in reply to: Gianluca Interlandi: "Re: query about wrapped coordinates"In reply to: Gianluca Interlandi: "Re: Force field design" Next in thread: Axel Kohlmeyer: "Re: Force field design" Reply: Axel Kohlmeyer: "Re: Force field design" Messages sorted by: [ attachment ] On 24 July 2014 22:22, Gianluca Interlandi <gianluca_at_u. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. edu> wrote: > Hi, > > I have a question concerning running NAMD on a CUDA cluster. Author Profile. washington. washington. Just a good MD toy ! Victor owner-namd-l_at_ks. , the force on the SMD atom gets huge. Neil King Assistant Professor. FimH consists of a pilin domain (PD) that anchors it to the rest of the fimbria and an allosterically regulated lectin domain (LD) that binds mannose on the. From: Gianluca Interlandi (gianluca_at_u. 1002/prot. We are building a smaller cluster though in the lab and will test the scalability2006/9/6, Gianluca Interlandi <gianluca_at_u. I would be > happy if somebody could point me out to some scripts which help me perform(no subject) From: BIPLAB NANDI (dafodils2002_at_gmail. Entertainment. Sunhwan On Jul 16, 2014, at 12:32 AM, Gianluca Interlandi <gianluca_at_u. You simply load your trajectory > into VMDReply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] So your speed for 1 or 2 GPUs (based on what your sent) is about 1. washington. 7b1 on NCSA. Bioengineering. 7 ns/day, which seems decent given the system size. washington. uiuc. washington. Whitfield, 2 Esther Bullitt, 4 Ronald E. > On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). . edu) Date: Thu Nov 02 2006 - 13:55:24 CST Next message: Ugur Akgun: "ABF on a single molecule" Previous message: Al-Rawi, Ahlam: "external force" In reply to: Al-Rawi, Ahlam: "external force" Next in thread: Gianluca Interlandi:. ch>: > Hi Nathalie, > > It seems that CHARMM doesn't read the residue number correctly: > > 2011/6/29 Gianluca Interlandi <gianluca_at_u. edu) Date: Thu Apr 05 2012 - 15:44:43 CDT Next message: Gianluca Interlandi: "Re: DCD" Previous message: Jérôme Hénin: "Re: changing harmonic restraints (colvars)" Next in thread: Gianluca Interlandi: "Re: DCD" Reply: Gianluca Interlandi: "Re: DCD" Messages sorted by: [ attachment ]. Reply: Gianluca Interlandi: "Re: Cuda benchmarks namd2. edu> wrote: > Hi Fatemeh, > > Thanks for replying. Re: Abe versus Lincoln. Usually, this > is > written in the dcd file if you specified "DCDUnitCell yes" in your > NAMD > config file. The Netherlands) is an antibody raised against K12 FimH-lectin domain (residues 1–160) and previously determined to recognize or induce the high affinity state of K12 FimH, especially in the presence of ligand ( buffer in wells of 96-well flat-bottom plates at 37 °C for 1 h. She joined Schiller DuCanto & Fleck LLP in 1999 as a law clerk and became partner with the firm in 2009. 122076 s/step, which is 16% slower than using > the 6Re: Question about equilibration. Gianluca On Thu, 31 May 2012, Kapil jain wrote: > Hi all, > I am running md simulation on homology model of a membrane protein, following the membrane > protein tutorial. edu) Date: Sat Apr 25 2009 - 12:05:17 CDT Next message: Gianluca Interlandi: "NAMD 2. There have been over 180 downloads and no complaints so far. I was getting 2. Reply: Gianluca Interlandi: ""wrapAll on" with a complex" Reply: Gianluca Interlandi: "Scale" Messages sorted by: [ attachment ] Dear NAMD users, I'm performing SMD simulations and I have problems when I restart a simulation, i. From: Gianluca Interlandi (gianluca_at_u. In the text > field you can enter your atom selection, e. edu > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. Re: replica exchange and GPU acceleration. From: Gianluca Interlandi (gianluca_at_u. 7 released. Deadline is this Friday (or in three > months). The other> Auftrag von Gianluca Interlandi > Gesendet: Sonntag, 27. Gianluca On Thu, 20 Feb 2014, Kenno Vanommeslaeghe wrote: > I likely don't know the answer to this, but just to clarify the question, you > are talking about an Xplor topology and/or parameter (not psf) file you want > to convert to a CHARMM topology and/or parameter file, right? > > On 02/20/2014 03:31 AM, Peter Reinke wrote: >> Dear all, >>Re: NAMD 2. Best, Jerome Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. Mechanism of allosteric propagation across a β-sheet structure investigated by molecular dynamics simulations. In the text field you can enter your atom selection, e. -Fatemeh On Fri, Dec 3, 2010 at 2:08 PM, Gianluca Interlandi < gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. ch +41 (0) 1 635 55 93SMD on center of mass. edu> wrote: > Hi, > > Can the current version of NAMD be used together with the new CHARMM36 force > field? The parameter files are "top_all36_prot. Maybe the file was not transferred correctly to your desktop PC. On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi < gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. 7 released. I needed to install the 'patch' program. > On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi <gianluca_at_u. washington. edu) Date: Thu Apr 05 2012 - 16:30:29 CDT Next message: Gianluca Interlandi: "RE: DCD" Previous message: Axel Kohlmeyer: "Re: DCD" In reply to: Buddhadev Maiti: "RE: DCD" Next in thread: Gianluca Interlandi: "RE: DCD" Reply: Gianluca Interlandi: "RE: DCD". washington. edu) Date: Thu Jul 16 2015 - 16:20:34 CDT Next message: Simon Kit Sang Chu: "Minimization without MD" Previous message: Gianluca Interlandi: "Re: namd ibverbs" In reply to: Gianluca Interlandi: "Re: namd ibverbs" Next in thread:. washington. washington. prm". 1 2 3 Barry Lutz starts tenure-track position, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professor UW Bioengineering is pleased to announce. Just a good MD toy ! Victor owner-namd-l_at_ks. , "not (water or ions)" GianlucaRe: DCD. washington. 26588 Item in Clipboard Cite. MyGianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. Re: Does Berendsen increase viscosity of water? From: Gianluca Interlandi (gianluca_at_u. 7b1 on Abe" Previous message: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" In reply to: Gianluca Interlandi: "Re: Yet another. From: Gianluca Interlandi (gianluca_at_u. washington. Next in thread: Gianluca Interlandi: "Re: Namd-I: Implicit solvent problem" Messages sorted by: [ attachment ] Hi Enrico. But, using the PBC my protein is continuous. Biochemistry. Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. Contact host. washington. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" Previous message: L. Choose File -> Save Coordinates. " >> Could a small damping coefficient lead to such errors? If so, what would >> be the scenarioGianluca On Sun, 30 Aug 2009, Axel Kohlmeyer wrote: > On Sun, 2009-08-30 at 12:11 -0700, Gianluca Interlandi wrote: >> Thank you Mike for sharing your information. Gianluca has 2 jobs listed on their profile. Name : Current Position : Tim Connolley, Bioengineering 2005 : Michigan State Mechanical Engineering Graduate Program: Brett Anderson, Bioengineering 2006Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of HealthCorrespondence to: Gianluca Interlandi, Department of Bioengineering, University of Washington Box 355061, 3720 15th Ave NE, Seattle, WA 98195-5061, USA. During the minimization and equilibriation with protein constrained, the > disulfide bond breaks. edu) Date: Thu Mar 17 2011 - 17:58:46 CDT Next message: Giacomo Fiorin: "Re: GBIS and ABF" Previous message: Branko: "GBIS and ABF" In reply to: Gianluca Interlandi: "Re: NAMD 2. 7 with the PLUMED patch" Messages sorted by: [ attachment ] I found the problem. You should simulate it in explicit water (or try one of the implicit From: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. (did you see if any hunk failed?) Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. C; the more troublesome part is the lack of long-range electrostatic treatments. edu> Subject: Re: namd-l: "wrapAll on" with a complex Gianluca: Using VMD with the attached script should solve that. >> >> According to your banchmarks, it looks like the less expensive GTX285 >> (around 300$) performs better than a Tesla C1060 which is 4 times more >> expensive. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi!One Bedroom Apartment, Sleeps 3 - £83 avg. Education/training Institution and location Dates attended Degree Conferred Field of studyGianluca On Sun, 30 Aug 2009, Gianluca Interlandi wrote: > Thanks Axel, > > I have also compared the cost of a GPU equiped PC versus a dual Quadcore PC. washington. e. Just source the Tcl file and use the 'unwrap' procedure. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. 6 version, although I am not running the cluster at full load yet. Department of Bioengineering, University of Washington, Seattle, Washington, 98195. washington. SASA in NAMD is used internally > to perform simulations in implicit solvent, whereas SASA in VMD is used to > analyse trajectories. edu> Date: Monday, May 7, 2007 7:26 pm Subject: Re: namd-l: query about wrapped coordinates > I have actually found a much easier way of adding the crystal > information > to your trajectory. edu] Sent: Thursday, April 05, 2012 5:04 PM To: Buddhadev Maiti Cc: Jérôme Hénin; namd-l_at_ks. From: Gianluca Interlandi (gianluca_at_u. edu] > Sent: Thursday, April 05, 2012 5:04 PM > To: Buddhadev Maiti > Cc: Jérôme Hénin; namd-l_at_ks. Semantic Scholar's Logo. edu> wrote: > A few of the simulations aborted with the following message: >> "ERROR: Atoms moving too fast; simulation has become unstable. Hope the video helps, but now I'm embarrassed. RE: Force field design. UW Bioengineering announces that Barry Lutz is hired as tenure-track faculty, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professorIn reply to: Gianluca Interlandi: "NAMD + nice" Messages sorted by: [ attachment ] Nice (process priority) is only supported in NET version of Charm++. washington. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). washington. washington. Next message: Gianluca Interlandi: "Infiniband and PME gridsize" Previous message: nordgren_at_sas. That's why one wants to use a low value for the damping constant, in principle. 0 and 2. Thomas, 2 , * and Evgeni V. Kisiela, # 1 , * Hovhannes Avagyan, # 1 Della Friend, 2 Aachal Jalan, 1 Shivani Gupta, 3 Gianluca Interlandi, 3 Yan Liu, 4 Veronika Tchesnokova, 1 Victoria. From: Axel Kohlmeyer (akohlmey_at_gmail. edu) Date: Fri May 01 2009 - 12:18:05 CDT Next message: Grace Brannigan: "Re: crash with more than 96 processors (v2. Just source the Tcl file and use the 'unwrap' procedure. com) Date: Wed Aug 27 2014 - 22:13:06 CDT Next message: Gianluca Interlandi: "Re:" Previous message: Douglas Houston: "Re: AW: Using nodelist file causes namd to hang" Next in thread: Gianluca Interlandi: "Re:" Reply: Gianluca Interlandi: "Re:" Messages sorted by: [. I would be > happy if somebody could point me out to some scripts which help me performOn Thu, 5 Apr 2012, Gianluca Interlandi wrote: > What is the advantage of the multicore version of charm++ versus net-linux? > Is multicore faster if I'm running for example on a 32-core magny-Cours AMDFrom: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. Search 214,979,228 papers from all fields of science. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on small> 2011/6/29 Gianluca Interlandi <gianluca_at_u. Next message: Gianluca Interlandi: "RE: Force field design" Previous message: Aron Broom: "Re: Force field design" In reply to: Abhishek TYAGI: "Force field design" Next in thread: Mayne, Christopher G: "Re: Force field design" Messages sorted by: [ attachment ] If you are familiar with the CHARMM program, a good resource is:. washington. From: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. -michael On Jun 15, 2006, at 5:31 PM, Gianluca Interlandi wrote:> 2011/6/29 Gianluca Interlandi <gianluca_at_u. > > Forget about creating a pdb file. washington. From: Gianluca Interlandi (gianluca_at_u. I needed to install the 'patch' program. 6 ns/day for a 100k atom system with roughly those same parameters (and. See more properties from this host. edu> > wrote:Re: Help building a desktop for namd. From: Gianluca Interlandi (gianluca_at_u. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. washington. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. edu> wrote: > Hi Fatemeh, >> On Wed, Dec 12, 2012 at 12:26 PM, Gianluca Interlandi <gianluca_at_u. washington. On Tue, 19 Oct 2010, Gianluca Interlandi wrote: > Hi Jim, > > This is great! Is there also a compiled version for Clustermatic 5? > > Thanks, > > Gianluca > > On Tue, 19 Oct 2010, Jim Phillips wrote: > >> Hi all, >> >> I pushed 2. Re: query about wrapped coordinates. edu) Date: Mon May 28 2007 - 10:33:29 CDT Next message: Gianluca Interlandi: "Re: Protein in/out of box" Previous message: Peter Freddolino: "Re: constraints on zinc ions" In reply to: Monika Sharma: "Protein in/out of box" Next in. 7b1 on NCSA Abe. From: Gianluca Interlandi (gianluca_at_u. I am > using the option "wrapAll on". edu> wrote: > Dear all, > > Does anybody have any recommendation how to convert a solvated system > (protein + solvent + ions) PDB + PSF from the CHARMM to the Amber force > field so that it can be used in NAMD with the Abmer force field Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. washington. Rachel Tsai 1 , Gianluca Interlandi 1 Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, USA. 478 KJ/mol = 0. From: bharat gupta (bharat. C; the more troublesome part is the lack of long-range electrostatic treatments. The only significant change since 2. From: Gianluca Interlandi <gianluca_at_u. 7 with the PLUMED patch" Messages sorted by: [ attachment ] I found the problem. However, using monoclonal antibodies specific for the mannose-binding Escherichia coli. SMD on center of mass. Gianluca Interlandi , Contributed equally to this work with: Pavel Aprikian, Gianluca Interlandi Affiliation Department of Bioengineering, University of Washington, Seattle, Washington, United. at 298. From: Gianluca Interlandi (gianluca_at_u. . Re: Vibrational mode analysis. Hope the video helps, but now I'm embarrassed. Eddie: "gentoo ebuild" Previous message: Robert Johnson: "Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes" Maybe in reply to: Norman Geist: "AW: AW: Running NAMD on Forge (CUDA)"Gianluca Interlandi, ‡, 1, 2 Olga Yakovenko, ‡, 1 An-Yue Tu,. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. Chemistry. > > gianluca, >Next in thread: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 5:21 PM, Gianluca Interlandi <gianluca_at_u. edu]Reply All Saturday,. Reply: Gianluca Interlandi: "Re: Regarding thermostats" Reply: Marcos Sotomayor: "Re: Regarding thermostats" Messages sorted by: [ attachment ] Dear NAMD users, Lately in the lab we have been discussing about which thermostat use in our simulations. washington. washington. unizh. 3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20). > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?On Mon, Aug 26, 2013 at 12:56 PM, Gianluca Interlandi < gianluca_at_u. ca) Date: Tue Oct 31 2023 - 20:31:14 CDT Next message: Gianluca Interlandi: "Re: VMD openGL over ssh from a server with NVIDIA" Previous message: Victor Kwan: "Re: VMD openGL over ssh from a server with NVIDIA" In reply to: Gianluca Interlandi: "Re: VMD openGL over ssh from a. GianlucaFrom: Gianluca Interlandi (gianluca_at_u. I > > attach a plot of a constant velocity simulation where I'm pulling twoRe: NAMD 2. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. Choose File -> Save Coordinates. PMID: 33550613 PMCID: PMC8089038 DOI: 10. edu) Date: Fri May 01 2009 - 12:18:05 CDT Next message: Grace Brannigan: "Re: crash with more than 96 processors (v2. Jennifer KongRE: DCD. 15 K 1 KT = 2. Gianluca Interlandi 1 , Minhua Ling, An Yue Tu, Dominic W Chung, Wendy E Thomas Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, United States of America. Sarah Keller Professor. washington. >Gianluca Interlandi (Property Manager Baroque Apartments) Hosting since October 2020. You should simulateCorresponding Author. I am > using the option "wrapAll on". washington. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" From: Gianluca Interlandi (gianluca_at_u. g. uiuc. edu > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. From: Gianluca Interlandi [gianluca_at_u. 6 version, although I am not running the cluster at full load yet. . washington. washington. Kitchen. > > > > I have already run a bunch of pulling simulations in the NVE ensemble. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). From: Gianluca Interlandi (gianluca_at_u. washington. Gianluca Interlandi Research Assistant Professor. washington. From: Gianluca Interlandi (gianluca_at_u. The simulations were not performed at constant velocity > but at constant force. Managing Member/Principal Atlantic Mortgage Partners, LLC Jun 2009 - Jun 2012 3 years 1. Gianluca Interlandi Foege N430E gianluca_at_uw_dot_edu My laboratory combines tools from computational structural biology, like molecular dynamics simulations and Monte Carlo methods, with biochemical and biophysical assays to unravel the molecular basis behind biological processes like the blood coagulation cascade and cellular adhesion. Bioengineering. washington. Previous message: Gianluca Interlandi: "NAMD 2. GianlucaHosted by Gianluca Interlandi. Policies. In reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. upenn. Thanks for the reply. edu) Date: Wed Jul 16 2014 - 00:32:49 CDT Next message: Sadegh Faramarzi Ganjabad: "Re:Subject: Re: Subject: Re:Re: New partial charges after patching" Previous message: Gianluca Interlandi: "Re: Force field design" Next in. Re: Help building a desktop for namd. washington. You should simulate it in explicit water (or try one of the implicitRe: Protein in/out of box. 0 and 2. 7b1 on Abe" In reply to: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" Messages sorted by: [ attachment ] The amount of computational work that you have for the nonbonded short-range interactions (which is the dominant part of the overallRe: Help building a desktop for namd. On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. edu) Date: Thu Apr 30 2009 - 12:15:37 CDT Next message: bo liu: "Re: Optimizing configuration option for fast calculations" Previous message: Jerome Henin: "Re: Benzene PSF" In reply to: Peter Freddolino: "Re: NAMD 2. g. /night - Ortigia - Amenities include: Internet, Air conditioning, TV, Satellite or cable, No smoking Bedrooms: 1 Sleeps: 3 Minimum stay: 2 night(s) Book online - Book holiday rental 11131246 with Vrbo. edu> wrote: > Dear all, > > Does anybody have experience simulating carbohydrates with NAMD? In > particular, I'm interested whether the CHARMM or the AMBER force field is > more accurate to simulate carbohydrates. Re: Yet another NAMD speed concerns. From: Gianluca Interlandi (gianluca_at_u. com) Date: Sat Jul 04 2015 - 10:49:22 CDT Next message: Gianluca Interlandi: "multicore vs ibverbs" Previous message: Josh Vermaas: "Re: extra bonds" Maybe in reply to: Mitchell Gleed: "Re: replica exchange and GPU acceleration" Next in. I know the lack of treatment of the hydrophobic part but the point here is the different results for same implicit solvent model. It's > slightly faster but still not that much faster than running on 16 CPU cores. edu] Sent: Monday, June 20, 2016 12:46 PM To: Richard Wood Cc: John Stone; vmd-l_at_ks. In reply to: Gianluca Interlandi: "Compiling NAMD 2. washington. 7b4 is thatRE: DCD. Search for: Main Menu. Re: external force. 7b1 on NCSA Abe. In reply to: Gianluca Interlandi: "Compiling NAMD 2. washington. > > > > Forget about creating a pdb file. From: Gianluca Interlandi (gianluca_at_u. edu) Date: Fri May 01 2009 - 12:18:05 CDT Next message: Grace Brannigan: "Re: crash with more than 96 processors (v2. > However, topology and parameters for water and ions are. 2020-10-26T08:31:24-07:00 September 9th, 2014 | Read More UW Bioengineering Summer Camp 2014 concludes, teaches high school students about bioengineering, global health. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi! Next in thread: Gianluca Interlandi: "Scale" Messages sorted by: [ attachment ] Gianluca: Using VMD with the attached script should solve that. Re: Abe versus Lincoln. Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. One of the two proteins has reached one of > the boundaries of the box and it has been wrapped around. E-mail: [email protected] > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. I'm > not sure whether the CHARMM program can read. Eddie: "gentoo ebuild" Previous message: Robert Johnson: "Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes" Maybe in reply to: Norman Geist: "AW: AW: Running NAMD on Forge (CUDA)"Re: namd ibverbs. 7 ns/day, which seems decent given the system size. Cancellation policy. washington. 2016. Hi I’m Yiming Li, and I’m a senior in bioengineering. Choose File -> Save Coordinates. > > NCSA Forge has for example 6 CUDA devices and 16 CPU cores per node. It's > slightly faster but still not that much faster than running on 16 CPU cores.