Re: [gmx-users] Updating GTX670 PCIE speed from 5GT/s to 8GT/s resulted in about 10% speedup of md_run.
Hi Henk, Thanks for the useful comments! When you run on a single GPU, you do get full timing details both on CPU and GPU - just have a look at the performance tables at the end of the log file. Alternatively you can simply run nvrpof mdrun which will by default give you a nice overview of profiling output of CUDA device and API calls. Regarding the performance improvement, I'm suspecting that you are probably seeing the full speed improvement that comes from 5GT/s-8GT/s because of the CPU-GPU load imbalance in your run - probably the CPU one is waiting 20% of the runtime for the GPU to finish. Hence, in these imbalanced cases any improvement on the GPU side - transfer or kernel -, will translate straight into decrease in wall-time. We are working on a few things that should improve performance in this scenario like using multiple weakly dependant non-bonded tasks to some transfer/kernel overlap; non-bonded task splitting for a better load balance. Cheers, -- Szilárd On Wed, Dec 4, 2013 at 8:28 AM, Henk Neefs henk.ne...@gmail.com wrote: Below information might be of interest to the Gromacs development/optimization team. What can we derive from the 10% md_run speedup when PCIE3.0 speed increases from 5GT/s-8GT/s? A 60% PCIE speed increase results in a 10% run time reduction. Hence about 10/60=17% of the run time gets spent in (non-overlapping) PCIE bus communication for this particular configuration and for this particular simulated molecular system. I'm refering to the non-overlapping part as this is the part that is not hidden by (not overlapped with) calculations. So changing the PCIE speed provides a (non-user-friendly) knob to the gromacs developers to estimate the part of the run time that is determined by the (non-overlapping) PCIE bus communication. Not sure whether the Nvidia CUDA profiling environment provides a better way to quantify this. In case there isn't a better way, above method is a poor man's flow (for which you likely need root access) to provide this quantification. -- Henk Neefs Gromacs user -- View this message in context: http://gromacs.5086.x6.nabble.com/Updating-GTX670-PCIE-speed-from-5GT-s-to-8GT-s-resulted-in-about-10-speedup-of-md-run-tp5012945p5013031.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] heating
Hi Kiana, I always heat from 5 K to 300 K with ref_t=300 (ending temp) and gen_temp=5 (starting temp). 5 K is as good as starting at 0 K for my systems. Hope that helps. Regards, On Wed, Dec 4, 2013 at 12:18 PM, kiana moghaddam ki_moghad...@yahoo.comwrote: Dear Jastin Thanks very much for your reply, when I heat system from 0 to 300 K with simulated annealing, ref_t =300 is correct? Best Regards On Tuesday, December 3, 2013 5:53 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/3/13 2:17 AM, kiana moghaddam wrote: Dear GMX Users I want to run NVT equilibration and NPT equilibration (after NVT) and want to increase temperature gradually i.e. from 0 to 300 K over 100 ps, but I have some questions about this process: when I use simulated annealing in NVT as following annealing_time = 0 15 30 45 60 80 100 annealing_temp = 0 50 100 150 200 250 300 I don't know how to change gen_temp. Should gen_temp be 0 or 300 K? Generating velocities and then immediately freezing (in the strictest of sense) the system is likely not going to be stable or effective because the thermostat will go haywire trying to compensate for such a drastic change in temperature. It is an interesting question, because how does one generate velocities at 0 K? Theoretically, there are none. I would suggest setting gen_temp to 0; you can check the .tpr (via gmxdump) to see if any velocities are present, but even if they are they should be very small and largely irrelevant. The annealing protocol will warm the system relatively quickly, so even after a few dynamics steps, you will have small velocities within the system. At the first time, I did not use simulated annealing. I prepared 7 mdp files that in the first mdp file, I set nsteps=0, gen_temp=0, ref_t=0, then I use the output from first NVT equilibration for the second input. I repeat this to reach 300 K (in the second step nsteps=7500(*0.002=15), gen_temp=50, ref_t=50). I 'm not sure whether this process is correct? Well, it works, but it's laborious and unnecessary because you're just manually doing what simulated annealing is doing. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to make OPLS forcefield?
Dear Gromacs User, I am the beginner using Gromacs. I have created polyethylene .gro and .top using http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg but in that .top, forcefield is gmx.ff/forcefield.itp. I want to simulate with OPLS forcefield. Please help me how to make or convert to OPLS ff. Thanks in advance. Mary. -- View this message in context: http://gromacs.5086.x6.nabble.com/How-to-make-OPLS-forcefield-tp5013033.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] rcoulomb, rvdw and rlist value
Dear Users I want to use parmbsc0 force field for DNA-ligand interaction. I want some information about value of rcoulomb, rvdw and rlist in mdp file during equilibration production steps. I set these values 1 nm . Is it correct? Best regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Atomistic Simulation
Hello users, After downloading the toluene.pdb file of a toluene molecule and its forcefield tolu.itp from Automated Topology Builder and saved in the root /usr/share/gromacs/top/gromos53a6.ff I use the next comand i order to convert the pdb format to .gro : *** bash g_pdb2gmx -f tolu.pdb -o tolu.gro -i tolu.itp Select the Force Field: From '/usr/share/gromacs/top': 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 7: AMBERGS force field (Garcia Sanbonmatsu, PNAS 99, 2782-2787, 2002) 8: CHARMM27 all-atom force field (with CMAP) - version 2.0 9: GROMOS96 43a1 force field 10: GROMOS96 43a2 force field (improved alkane dihedrals) 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 15: [DEPRECATED] Encad all-atom force field, using full solvent charges 16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges 17: [DEPRECATED] Gromacs force field (see manual) 18: [DEPRECATED] Gromacs force field with hydrogens for NMR 13 Using the Gromos53a6 force field in directory gromos53a6.ff Opening force field file /usr/share/gromacs/top/gromos53a6.ff/watermodels.dat Select the Water Model: 1: SPCsimple point charge, recommended 2: SPC/E extended simple point charge 3: None 3 Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b Reading tolu.pdb... WARNING: all CONECT records are ignored Read 'ALL ATOM STRUCTURE FOR MOLECULE 0', 15 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 0 residues with 15 atoms chain #res #atoms 1 ' ' 1 15 All occupancies are one Opening force field file /usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp Atomtype 1 Reading residue database... (gromos53a6) Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 108 Sorting it all out... Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.7# Processing chain 1 (15 atoms, 1 residues) Warning: Starting residue _I0L0 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program g_pdb2gmx, VERSION 4.5.7 Source code file: /builddir/build/BUILD/gromacs-4.5.7/src/kernel/resall.c, line: 581 Fatal error: Residue '_I0L' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- You Own the Sun (Throwing Muses) * I checked the residue _I0L and is defined in the tolu.itp Why do I get this error? Am I missing something?? Thanks in advance!! Sergio -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013044.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] out of disk space error
On 12/4/13 5:24 AM, a...@imtech.res.in wrote: I think so. You are outputting the information too often i.e every 0.2 ps i.e. 5000 times per ns. See this thread http://comments.gmane.org/gmane.science.biology.gromacs.user/32721 It is unlikely that a few hundred ps of NVT would fill up someone's disk if it has several hundred GB available, but it can't hurt to reduce the output a bit. Frequent writing could be taxing the filesystem unnecessarily. It is also important to keep in mind that some desktop computers simply cannot handle a simulation that would be best run on a cluster with high-performance I/O. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Atomistic Simulation
On 12/4/13 6:15 AM, panzu wrote: Hello users, After downloading the toluene.pdb file of a toluene molecule and its forcefield tolu.itp from Automated Topology Builder and saved in the root /usr/share/gromacs/top/gromos53a6.ff I use the next comand i order to convert the pdb format to .gro : *** bash g_pdb2gmx -f tolu.pdb -o tolu.gro -i tolu.itp Select the Force Field: From '/usr/share/gromacs/top': 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 7: AMBERGS force field (Garcia Sanbonmatsu, PNAS 99, 2782-2787, 2002) 8: CHARMM27 all-atom force field (with CMAP) - version 2.0 9: GROMOS96 43a1 force field 10: GROMOS96 43a2 force field (improved alkane dihedrals) 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 15: [DEPRECATED] Encad all-atom force field, using full solvent charges 16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges 17: [DEPRECATED] Gromacs force field (see manual) 18: [DEPRECATED] Gromacs force field with hydrogens for NMR 13 Using the Gromos53a6 force field in directory gromos53a6.ff Opening force field file /usr/share/gromacs/top/gromos53a6.ff/watermodels.dat Select the Water Model: 1: SPCsimple point charge, recommended 2: SPC/E extended simple point charge 3: None 3 Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b Reading tolu.pdb... WARNING: all CONECT records are ignored Read 'ALL ATOM STRUCTURE FOR MOLECULE 0', 15 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 0 residues with 15 atoms chain #res #atoms 1 ' ' 1 15 All occupancies are one Opening force field file /usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp Atomtype 1 Reading residue database... (gromos53a6) Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 108 Sorting it all out... Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.7# Processing chain 1 (15 atoms, 1 residues) Warning: Starting residue _I0L0 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program g_pdb2gmx, VERSION 4.5.7 Source code file: /builddir/build/BUILD/gromacs-4.5.7/src/kernel/resall.c, line: 581 Fatal error: Residue '_I0L' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- You Own the Sun (Throwing Muses) * I checked the residue _I0L and is defined in the tolu.itp Why do I get this error? Am I missing something?? Why are you running pdb2gmx? ATB provides you with the topology that you need. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit
Re: [gmx-users] GROMACS 4.6.5 is released
On Wed, Dec 4, 2013 at 10:15 AM, João Henriques joao.henriques.32...@gmail.com wrote: Soon enough we will have daily releases :P I hope you're not suggesting that we should release less frequently! :) Mark, can you please elaborate just a tiny bit longer on how relevant were the GPU-load balancing and GPU-sharing bugs introduced in a bug fix in 4.6.4? I'm asking this because I just requested the support team at my local cluster to install 4.6.4 and I don't have the nerve to request another install so soon. As always, read the release notes and if interested in details, links to the redmine page of bugs are listed there as well: http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x Cheers, -- Szilárd Cheers, /J On Tue, Dec 3, 2013 at 12:41 AM, Mark Abraham mark.j.abra...@gmail.comwrote: Hi GROMACS users, GROMACS 4.6.5 is officially released. It contains a significant bug fix when using GPUs in a multi-node simulation, introduced in another recent bug fix. We encourage all users to upgrade their installations from earlier 4.6.x releases. You can find the code, manual, release notes, installation instructions and test suite at the links below. Note that the tests and manual have not changed since 4.6.4. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.5.tar.gz ftp://ftp.gromacs.org/pub/manual/manual-4.6.5.pdf http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x#Release_notes_for_4.6.5 http://www.gromacs.org/Documentation/Installation_Instructions http://gromacs.googlecode.com/files/regressiontests-4.6.5.tar.gz Happy simulating! Mark Abraham GROMACS development manager -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Atomistic Simulation
so How do I convert from .pdb to .gro? -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013059.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Atomistic Simulation
On 12/4/13 9:06 AM, panzu wrote: so How do I convert from .pdb to .gro the ? You don't technically need one: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File If you prefer to use .gro format, just convert with editconf. The job of pdb2gmx is to produce a topology; the output of a force field-compliant structure is a side effect. You already have a matching structure and a topology, so there's no need to run pdb2gmx. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GROMACS 4.6.5 is released
I did read it and wasn't very enlightened by it, that's why I kindly requested for further information on the subject. under certain circumstances (but quite often), a segmentation fault occurs definitely sounds serious, but it's not very explicit. In any case, I'll request a new install and tell them to remove the previous version form the cluster. We don't want segmentation faults to happen under certain circumstances :) Thank you, /J On Wed, Dec 4, 2013 at 2:27 PM, Szilárd Páll pall.szil...@gmail.com wrote: On Wed, Dec 4, 2013 at 10:15 AM, João Henriques joao.henriques.32...@gmail.com wrote: Soon enough we will have daily releases :P I hope you're not suggesting that we should release less frequently! :) Mark, can you please elaborate just a tiny bit longer on how relevant were the GPU-load balancing and GPU-sharing bugs introduced in a bug fix in 4.6.4? I'm asking this because I just requested the support team at my local cluster to install 4.6.4 and I don't have the nerve to request another install so soon. As always, read the release notes and if interested in details, links to the redmine page of bugs are listed there as well: http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x Cheers, -- Szilárd Cheers, /J On Tue, Dec 3, 2013 at 12:41 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi GROMACS users, GROMACS 4.6.5 is officially released. It contains a significant bug fix when using GPUs in a multi-node simulation, introduced in another recent bug fix. We encourage all users to upgrade their installations from earlier 4.6.x releases. You can find the code, manual, release notes, installation instructions and test suite at the links below. Note that the tests and manual have not changed since 4.6.4. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.5.tar.gz ftp://ftp.gromacs.org/pub/manual/manual-4.6.5.pdf http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x#Release_notes_for_4.6.5 http://www.gromacs.org/Documentation/Installation_Instructions http://gromacs.googlecode.com/files/regressiontests-4.6.5.tar.gz Happy simulating! Mark Abraham GROMACS development manager -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] flags for internal coordinates restraints
LINCS or SHAKE (all atoms) can be used for this? or some better options available? it can be seen as two protein helix interacting with each other as rigid bodies... thanks On Wed, Nov 27, 2013 at 12:35 AM, gromacs query gromacsqu...@gmail.comwrote: Dear All I want to simulate two polymer chains as rigid bodies, in other words allowing two polymer to interact with each other but keeping their internal coordinates restrained. Also it can be seen as two rods interacting with each other. Which flags/options can be used in Gromacs? regards JIomm -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] atom name - topology
On 12/4/13 11:48 AM, Steven Neumann wrote: Dear Gmx Users, My molecule contains 2516 atoms made of 5 type of beads: BAS, POL, NON, ACI, GLY and I want to create a topology. Is it possible to make one residue of one [ moleculetype ] with this number of atoms so that: [ moleculetype ] ; Namenrexcl MOL3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB ; residue 1 1N rtp 1N q 0.0 1BAS11N110133.208 2POL11N22087.08 3NON11N330147.172 4BAS11N440157.204 5POL11N55087.08 ... 2500 POL11N25005087.08 Can atom column contain number from 1 to 2500? Have you tried it? Are you getting some problem? IIRC the atom column requires a string (name), not an integer. That's what the atom number column is for. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] force field for prodrg server
dear Justin thanks for reply I don't find tutorial for ATB and I don't know that which files are used for itp and gro files from ATB result, Moreover in gromacs site is mentioned that PRODRG is used for GROMOS96 force field, 43A1. can I use ATB for 43A1 force field? On Wednesday, December 4, 2013 7:07 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/4/13 10:24 AM, Mahboobeh Eslami wrote: hi dear Justin You've written the following context in your tutorial: Force field (GROMOS96.1/GROMOS87): GROMOS96.1 refers to the first version of the GROMOS96 force field, 43A1. GROMOS87 refers to the (outdated!) GROMOS87 force field. Choose GROMOS96.1 to get 43A1 parameters for our ligand but I don't see the option for Select the force field in PRODRG server PRODRG is now hosted by a company, so I don't know what sorts of changes they have introduced. There is no more force field selection, so it's a black box, I suppose. Given that you probably have to re-write the topology anyway, it probably doesn't matter much except for a few atom types that may be different between the force fields. ATB is probably a better option; I think its output is generally much more reliable than PRODRG. I'll probably revise the tutorial at some point, but the use of PRODRG to get a flawed topology is a good teaching tool. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] out of disk space error
If none of the earlier suggestions worked then, it could be a simple problem of power port from which you have connected your hard disk. Try reconnecting the hard disk and and retry running the mdrun. Posting the exact commands used while writing the output during mdrun, may help to trace the problem. On Thu, Dec 5, 2013 at 11:03 AM, vaani vsha...@imtech.res.in wrote: On 12/4/13 5:24 AM, amin@.res wrote: I think so. You are outputting the information too often i.e every 0.2 ps i.e. 5000 times per ns. See this thread http://comments.gmane.org/gmane.science.biology.gromacs.user/32721 It is unlikely that a few hundred ps of NVT would fill up someone's disk if it has several hundred GB available, but it can't hurt to reduce the output a bit. Frequent writing could be taxing the filesystem unnecessarily. It is also important to keep in mind that some desktop computers simply cannot handle a simulation that would be best run on a cluster with high-performance I/O. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 hi justin, i have already run simulations on this work station before also without any such disk space problem. i am facing this problem now only after installing ubuntu and gromacs freshly, best - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013086.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- *Thanks and Regards,Bipin Singh* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GROMACS 4.6.5 is released
The first update on the redmine page does describe the source of the issue - although perhaps not in the most user-friendly manner. Translating it to a simple example, if you have dual-socket 8c nodes and 2 GPUs per node: mpirun -np 4 mdrun -ntomp 4 -gpu_id 0011 #single node 4 ranks per node, 2-way rank-GPU sharing mpirun -np 4 mdrun -ntomp 8 -gpu_id 01 #two nodes 2 ranks per node, no GPU sharing will work, but mpirun -np 8 mdrun -ntomp 4 -gpu_id 0011 #two nodes 4 ranks per node, 2-way rank-GPU sharing will crash. Cheers -- Szilárd On Wed, Dec 4, 2013 at 5:38 PM, João Henriques joao.henriques.32...@gmail.com wrote: I did read it and wasn't very enlightened by it, that's why I kindly requested for further information on the subject. under certain circumstances (but quite often), a segmentation fault occurs definitely sounds serious, but it's not very explicit. In any case, I'll request a new install and tell them to remove the previous version form the cluster. We don't want segmentation faults to happen under certain circumstances :) Thank you, /J On Wed, Dec 4, 2013 at 2:27 PM, Szilárd Páll pall.szil...@gmail.com wrote: On Wed, Dec 4, 2013 at 10:15 AM, João Henriques joao.henriques.32...@gmail.com wrote: Soon enough we will have daily releases :P I hope you're not suggesting that we should release less frequently! :) Mark, can you please elaborate just a tiny bit longer on how relevant were the GPU-load balancing and GPU-sharing bugs introduced in a bug fix in 4.6.4? I'm asking this because I just requested the support team at my local cluster to install 4.6.4 and I don't have the nerve to request another install so soon. As always, read the release notes and if interested in details, links to the redmine page of bugs are listed there as well: http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x Cheers, -- Szilárd Cheers, /J On Tue, Dec 3, 2013 at 12:41 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi GROMACS users, GROMACS 4.6.5 is officially released. It contains a significant bug fix when using GPUs in a multi-node simulation, introduced in another recent bug fix. We encourage all users to upgrade their installations from earlier 4.6.x releases. You can find the code, manual, release notes, installation instructions and test suite at the links below. Note that the tests and manual have not changed since 4.6.4. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.5.tar.gz ftp://ftp.gromacs.org/pub/manual/manual-4.6.5.pdf http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x#Release_notes_for_4.6.5 http://www.gromacs.org/Documentation/Installation_Instructions http://gromacs.googlecode.com/files/regressiontests-4.6.5.tar.gz Happy simulating! Mark Abraham GROMACS development manager -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
