[gmx-users] Hydrophobic interactions and electrostatic interactions between the protein chains
Hi dear GROMACS usersI want to calculate hydrophobic interactions and electrostatic interactions between the protein chains using gromacs trajectory . Please guide me.Thanks a lot -- 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] VMD movie making-remove water molecules from .trr after a simulation
Thank you Justin. Is it possible to choose protein and ligand separately (e.g. 1|13) in the trjconv, since I chose protein-ligand subgroup which was taken as a whole and ligand can not be distinguished individually ? Or should I do any modifications in VMD ? On Monday, March 11, 2019, 6:32:22 PM EDT, Justin Lemkul wrote: On 3/11/19 6:01 PM, mary ko wrote: > Dear all > How can I make a movie from a protein-ligand simulation in VMD? I opened > complex.pdb and md-fit.trr and the movie is shown but due to the large > number of water molecules it freezes after some frames. How can I remove > solvent molecules from the md-fit.trr? Any other suggestions how to make the > movie without freezing? Use trjconv to save whatever subset of coordinates you want. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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] gmx trjconv trr xtc
.trr and .xtc are two different file formats, with the latter being compressed. Therefore, an .xtc file will be significantly smaller than a .trr Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Tue, 12 Mar 2019 at 10:56, Alex wrote: > Dear groamcs user, > A system of mine contains two molecule type of A and B in water. Using > gmx trjconv -f out.xtc -o out.last.5ns.trr I first truncated the last 5ns > of the system's XTC file as a TRR file and just selected the non-water > contents so that the TRR file only has A and B. The TRR file is 4.4 GB. > Then I applied again the "gmx trjconv -pbc cluster -center yes -f > out.last.5ns.trr -o out.last.5ns.xtc" and again just non-water was chosen. > I was expecting that the both out.last.5ns.trr and out.last.5ns.xtc would > have the same size 4.4 GB as the material in both of them are just A and B, > however, the out.last.5ns.xtc is just 1.4 GB! > I wonder if that is normal? here I just care about the coordinates > dynamically and not velocity, do you think I am loosing any coordinate in > by the second command from out.last.5ns.trr to out.last.5ns.xtc? > > Regards > Alex > -- > 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.
[gmx-users] gmx trjconv trr xtc
Dear groamcs user, A system of mine contains two molecule type of A and B in water. Using gmx trjconv -f out.xtc -o out.last.5ns.trr I first truncated the last 5ns of the system's XTC file as a TRR file and just selected the non-water contents so that the TRR file only has A and B. The TRR file is 4.4 GB. Then I applied again the "gmx trjconv -pbc cluster -center yes -f out.last.5ns.trr -o out.last.5ns.xtc" and again just non-water was chosen. I was expecting that the both out.last.5ns.trr and out.last.5ns.xtc would have the same size 4.4 GB as the material in both of them are just A and B, however, the out.last.5ns.xtc is just 1.4 GB! I wonder if that is normal? here I just care about the coordinates dynamically and not velocity, do you think I am loosing any coordinate in by the second command from out.last.5ns.trr to out.last.5ns.xtc? Regards Alex -- 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] VMD movie making-remove water molecules from .trr after a simulation
On 3/11/19 6:01 PM, mary ko wrote: Dear all How can I make a movie from a protein-ligand simulation in VMD? I opened complex.pdb and md-fit.trr and the movie is shown but due to the large number of water molecules it freezes after some frames. How can I remove solvent molecules from the md-fit.trr? Any other suggestions how to make the movie without freezing? Use trjconv to save whatever subset of coordinates you want. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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] gromacs error in vacuum preparation simulation
On 3/11/19 5:45 PM, Mario Andres Rodriguez Pineda wrote: If i don't use -maxwarn option they send me the same error. Omitting -maxwarn won't fix problems, but it is a very bad habit to casually use -maxwarn as it overrides critical problems with your input. I see also this: WARNING 1 [file topol.top, line 23986]: You are using Ewald electrostatics in a system with net charge. This can lead to severe artifacts, such as ions moving into regions with low dielectric, due to the uniform background charge. We suggest to neutralize your system with counter ions, possibly in combination with a physiological salt concentration. Cheking the archive toppol.top this line is empty I'm try to minimize the energy of my protein in vacum, whithout ions or solvent As the message says, you shouldn't be using PME for this system. In vacuum, you should be using plain cutoff electrostatics with infinite cutoffs (rlist=rcoulomb=rvdw=0). -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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] VMD movie making-remove water molecules from .trr after a simulation
Dear all How can I make a movie from a protein-ligand simulation in VMD? I opened complex.pdb and md-fit.trr and the movie is shown but due to the large number of water molecules it freezes after some frames. How can I remove solvent molecules from the md-fit.trr? Any other suggestions how to make the movie without freezing? Thank you. -- 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 error in vacuum preparation simulation
If i don't use -maxwarn option they send me the same error. I see also this: WARNING 1 [file topol.top, line 23986]: You are using Ewald electrostatics in a system with net charge. This can lead to severe artifacts, such as ions moving into regions with low dielectric, due to the uniform background charge. We suggest to neutralize your system with counter ions, possibly in combination with a physiological salt concentration. Cheking the archive toppol.top this line is empty I'm try to minimize the energy of my protein in vacum, whithout ions or solvent Em seg, 11 de mar de 2019 às 17:12, Justin Lemkul escreveu: > > > On 3/11/19 3:20 PM, Mario Andres Rodriguez Pineda wrote: > > Hi everybody > > I want to do one dynamic simulation of one protein > > i'm try to minimize the protein in vacum before the simulation runing but > > gromacs send me this error: > > --- > > Program: gmx grompp, version 2018.6 > > Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1991) > > > > Fatal error: > > There was 1 error in input file(s) > > > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > --- > > > -- > > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > > with errorcode 1. > > > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > > You may or may not see output from other processes, depending on > > exactly when Open MPI kills them. > > > -- > > this is the command that i use for minimization in vacum. > > gmx_mpi grompp -f vacuum.mdp -c cbd212_box.gro -p topol.top -o > > cbd212_vac.tpr -maxwarn 1 > > Run grompp interactively if you want to see the actual error. It may > also be printed to a log file from your queuing system. Also, never use > -maxwarn. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.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. > -- *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* *Estudiante Doctorado en Biotecnología* *UNAL- MEDELLÍN/ IQ- USP* *Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas * *Av. Prof. Lineu Prestes 748, Sao Paulo SP, 05508-000, Tel: + 55 11 3091 1475* -- 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 error in vacuum preparation simulation
On 3/11/19 3:20 PM, Mario Andres Rodriguez Pineda wrote: Hi everybody I want to do one dynamic simulation of one protein i'm try to minimize the protein in vacum before the simulation runing but gromacs send me this error: --- Program: gmx grompp, version 2018.6 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1991) Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- this is the command that i use for minimization in vacum. gmx_mpi grompp -f vacuum.mdp -c cbd212_box.gro -p topol.top -o cbd212_vac.tpr -maxwarn 1 Run grompp interactively if you want to see the actual error. It may also be printed to a log file from your queuing system. Also, never use -maxwarn. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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] gromacs error in vacuum preparation simulation
Hi everybody I want to do one dynamic simulation of one protein i'm try to minimize the protein in vacum before the simulation runing but gromacs send me this error: --- Program: gmx grompp, version 2018.6 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1991) Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- this is the command that i use for minimization in vacum. gmx_mpi grompp -f vacuum.mdp -c cbd212_box.gro -p topol.top -o cbd212_vac.tpr -maxwarn 1 I can't find the solution for this problem. Thanks for your help -- *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* *Estudiante Doctorado en Biotecnología* *UNAL- MEDELLÍN/ IQ- USP* *Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas * *Av. Prof. Lineu Prestes 748, Sao Paulo SP, 05508-000, Tel: + 55 11 3091 1475* -- 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] grompp is using a very large amount of memory on a modestly-sized system
Hi, Mark, I'd be happy to, as soon as I get a chance. I know very little about how GROMACS works internally, but I had a few ideas I wanted to share in the hopes that they might help. One is that pairwise parameters for electrostatics could be implemented in the same way that LJ parameters are stored. That would provide a tremendous amount of flexibility for use cases far beyond my own. Or there could simply be an FEP flag for only scaling between molecule types, rather than also between molecules of a given type. Again, you guys are the experts and I know you have other priorities. Just my thoughts. Best, Sean On Fri, Mar 8, 2019 at 3:44 PM Mark Abraham wrote: > Hi, > > I don't have a solution for the question at hand, but it'd be great to have > your inputs attached to a new issue at https://redmine.gromacs.org, so > that > we can have such an input case to test with, so that we can improve the > simplistic implementation! Please upload it if you can. > > Mark > > On Fri., 8 Mar. 2019, 19:24 Sean Marks, wrote: > > > Scratch that comment about sparseness. I am short on sleep, and for a > > moment thought I was talking about constraints, not electrostatics. > > > > On Fri, Mar 8, 2019 at 1:12 PM Sean Marks > wrote: > > > > > I understand now, thank you for the prompt response. While the matrix > > > would actually be quite sparse (since the constraints are localized to > > each > > > ice molecule), I take it that memory is being allocated for a dense > > matrix. > > > > > > That aside, is it feasible to accomplish my stated goal of scaling > > > ice-water electrostatics while leaving other interactions unaffected? > One > > > alternative I considered was manually scaling down the charges > > themselves, > > > but doing this causes the lattice to lose its form. > > > > > > On Fri, Mar 8, 2019 at 12:28 PM Justin Lemkul wrote: > > > > > >> > > >> > > >> On 3/8/19 11:04 AM, Sean Marks wrote: > > >> > Hi, everyone, > > >> > > > >> > I am running into an issue where grompp is using a tremendous amount > > of > > >> > memory and crashing, even though my system is not especially large > > >> (63976 > > >> > atoms). > > >> > > > >> > I am using GROMACS 2016.3. > > >> > > > >> > My system consists of liquid water (7,930 molecules) next to a block > > of > > >> ice > > >> > (8,094 molecules). The ice oxygens are restrained to their lattice > > >> position > > >> > with a harmonic potential with strength k = 4,000 kJ/mol/nm^2. I am > > >> using > > >> > the TIP4P/Ice model, which is a rigid 4-site model with a negative > > >> partial > > >> > charge located on a virtual site rather than the oxygen. > > >> > > > >> > My goal is to systematically reduce the electrostatic interactions > > >> between > > >> > the water molecules and the position-restrained ice, while leaving > > >> > water-water and ice-ice interactions unaffected. > > >> > > > >> > To accomplish this, I am modeling all of the ice molecules using a > > >> single > > >> > moleculetype so that I can take advantages of GROMACS' FEP features > to > > >> > selectively scale interactions. I explicitly specify all constraints > > and > > >> > exclusions in the topology file. This moleculetype contains one > > virtual > > >> > site, 3 constraints, and 4 exclusions per "residue" (ice molecule). > > >> > > > >> > When I run grompp, I receive the following error, which I think > means > > >> that > > >> > a huge block of memory (~9 GB) was requested but could not be > > allocated: > > >> > > > >> > = > > >> > Command line: > > >> >gmx grompp -f npt.mdp -c md.gro -p topol.top -n index.ndx -r > > >> > initconf_packmol.gro -o input.tpr -maxwarn 2 -pp processed.top > > >> > > > >> > ... > > >> > > > >> > Generated 21 of the 21 non-bonded parameter combinations > > >> > Generating 1-4 interactions: fudge = 0.5 > > >> > Generated 21 of the 21 1-4 parameter combinations > > >> > Excluding 3 bonded neighbours molecule type 'ICE' > > >> > turning H bonds into constraints... > > >> > Excluding 3 bonded neighbours molecule type 'SOL' > > >> > turning H bonds into constraints... > > >> > Coupling 1 copies of molecule type 'ICE' > > >> > Setting gen_seed to 1021640799 > > >> > Velocities were taken from a Maxwell distribution at 273 K > > >> > Cleaning up constraints and constant bonded interactions with > virtual > > >> sites > > >> > Removing all charge groups because cutoff-scheme=Verlet > > >> > > > >> > --- > > >> > Program: gmx grompp, version 2016.3 > > >> > Source file: src/gromacs/utility/smalloc.cpp (line 226) > > >> > > > >> > Fatal error: > > >> > Not enough memory. Failed to realloc -8589934588 bytes for > il->iatoms, > > >> > il->iatoms=25e55010 > > >> > (called from file > > >> > > > >> > > > /home/semarks/source/gromacs/2016.3/icc/serial/gromacs-2016.3/src/gromacs/ > > >> > gmxpreprocess/convparm.cpp, > > >> > line 565) > > >> > > > >> > For more information and tips for troubleshooting,
Re: [gmx-users] gmx analyze -av
On 3/11/19 2:08 PM, Amin Rouy wrote: Hi, I notice that the flag ''-av'' in gmx analyze does not give the average value of the set, rather the data file itself. As it should. From gmx help analyze: "Option -av produces the average over the sets." If you want the average of different sets, just use gmx analyze -f. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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] gmx analyze -av
Hi, I notice that the flag ''-av'' in gmx analyze does not give the average value of the set, rather the data file itself. -- 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] Simulation crashed - Large VCM, Pressure scaling more than 1%, Bond length not finite
Thanks a lot, Kevin for your comments and help. Zeineb -- 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] Build a .top file
Hello, So i'm starting to learn about MD simulations and i've done the tutorial of Lysozyme in Water for Gromacs, my work is to do MD simulations for sugars using the tool do_glycans and the force field Glycam06, however i don't know how to generate the .top file? i would appreciate it if you could help me with that -- *Monia KAMLY,* *Ingénieur en Chimie Analytique et Instrumentation,* *Etudiante Master 2 Chimie, Spécialité, Agro-ressources Biomolécules et Innovations* *Faculté des Sciences et Techniques, Université de Limoges.* *123 Avenue Albert Thomas, 87000 Limoges* *Mobile: 06 99 78 86 29* *Email: monia.ka...@etu.unilim.fr * -- 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] pinoffset w LINCS error
Hi, I have two servers with AMD2950X (16 physical cores). One with 16Gb RAM and RTX2080Ti, the other 32Gb RAM and GTX1080Ti. I use gromacs 2018.3, compiled on the same way on both of the servers. I wanted to run two simulations on the same host (8+8cores and GPU0 and GPU1). They are OK on the 32GbRAM and GTX1080Ti computer. * One job with pinoffset fails on the 16Gb computer with LINCS errors. It runs without problem without pinoffset. * If I run only a single job but with pinoffset then it also fails. The error in case: cannot settle water molecule These indicate for me that memory, file naming, and setting parameters (pinoffset, gpuid) are OK and some magical problem exists. Do you have any suggestion? Thanks, Tamas -- Tamas Hegedus, PhD Senior Research Fellow Department of Biophysics and Radiation Biology Semmelweis University | phone: (36) 1-459 1500/60233 Tuzolto utca 37-47| mailto:ta...@hegelab.org Budapest, 1094, Hungary | http://www.hegelab.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.
[gmx-users] Gomacs 2019 build on sles12 and centos
Hi All, I've built Gromacs 2019 on both a CentOS 7 and SLES12 machine. Built using gcc@7.2.0 Dependencies: fftw@3.3.8 openmpi@3.1.3 When running "make check" on both machines, I'm getting the same timeout error for test 29 - see below for extract and attached for full test output anyone got any ideas? Thanks, Chris. === 29/40 Test #29: GmxPreprocessTests ...***Timeout 30.15 sec [==] Running 26 tests from 4 test cases. [--] Global test environment set-up. [--] 4 tests from GenconfTest [ RUN ] GenconfTest.nbox_Works [ OK ] GenconfTest.nbox_Works (186 ms) [ RUN ] GenconfTest.nbox_norenumber_Works [ OK ] GenconfTest.nbox_norenumber_Works (92 ms) [ RUN ] GenconfTest.nbox_dist_Works [ OK ] GenconfTest.nbox_dist_Works (372 ms) [ RUN ] GenconfTest.nbox_rot_Works center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 [ OK ] GenconfTest.nbox_rot_Works (471 ms) [--] 4 tests from GenconfTest (1121 ms total) [--] 5 tests from InsertMoleculesTest [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration Reading solute configuration Reading molecule configuration Initialising inter-atomic distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. The information in this email and in any attachment(s) is commercial in confidence. If you are not the named addressee(s) or if you receive this email in error then any distribution, copying or use of this communication or the information in it is strictly prohibited. Please notify us immediately by email at admin.internet(at)awe.co.uk, and then delete this message from your computer. While attachments are virus checked, AWE plc does not accept any liability in respect of any virus which is not detected. AWE Plc Registered in England and Wales Registration No 02763902 AWE, Aldermaston, Reading, RG7 4PR sprucea5:spack-build>make check [100%] Running all tests except physical validation /scratch/prod-spruce/acs/spack/opt/linux-sles12-x86_64/gcc-7.2.0/cmake-3.13.4-ocbi3jb2k4zbyt2lx7yvrm2ysb65nix6/bin/ctest --output-on-failure -E physicalvalidationtests Test project /ROWAN/group/pts/spack/dev-2019-02-19/var/spack/stage/gromacs-2019-55qcdjpc4twm5abmvt4kghka3eanxdc6/gromacs-2019/spack-build Start 1: TestUtilsUnitTests 1/40 Test #1: TestUtilsUnitTests ... Passed1.99 sec Start 2: TestUtilsMpiUnitTests 2/40 Test #2: TestUtilsMpiUnitTests Passed0.41 sec Start 3: MdlibUnitTest 3/40 Test #3: MdlibUnitTest Passed0.39 sec Start 4: AppliedForcesUnitTest 4/40 Test #4: AppliedForcesUnitTest Passed2.24 sec Start 5: ListedForcesTest 5/40 Test #5: ListedForcesTest . Passed1.29 sec Start 6: CommandLineUnitTests 6/40 Test #6: CommandLineUnitTests . Passed0.42 sec Start 7: DomDecTests 7/40 Test #7: DomDecTests .. Passed0.24 sec Start 8: EwaldUnitTests 8/40 Test #8: EwaldUnitTests ... Passed9.78 sec Start 9: FFTUnitTests 9/40 Test #9: FFTUnitTests . Passed0.48 sec Start 10: GpuUtilsUnitTests 10/40 Test #10: GpuUtilsUnitTests Passed0.23 sec Start 11: HardwareUnitTests 11/40 Test #11: HardwareUnitTests Passed0.24 sec Start 12: MathUnitTests 12/40 Test #12: MathUnitTests Passed4.02 sec Start 13: MdrunUtilityUnitTests 13/40 Test #13: MdrunUtilityUnitTests Passed0.25 sec Start 14: MdrunUtilityMpiUnitTests 14/40 Test #14: MdrunUtilityMpiUnitTests . Passed0.27 sec Start 15: OnlineHelpUnitTests 15/40 Test #15: OnlineHelpUnitTests .. Passed0.53 sec Start 16: OptionsUnitTests 16/40 Test #16: OptionsUnitTests . Passed2.04 sec Start 17: RandomUnitTests 17/40 Test #17: RandomUnitTests .. Passed0.50 sec Start
