[gmx-users] temperatures of residues
Dear all, I am going to calculate the temperature distribution inside a protein (temperatures of residues). Is there any command in gromacs to do that? Any suggestion is appreciated. Bests, Mohyeddin -- 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] Membrane simulation npt problem
The problem is outside your parameter file. On Fri, Jan 15, 2016 at 3:56 PM, Marco Franzoi wrote: > Good evening to everyone. > > I've an issue regarding a membrane simulation. > I've downloaded an already equilibrated POPE/POPG membrane and, to test the > system, I run an em, a 0.1 ns nvt and 1 ns npt simulation and everything > was fine. > > Then, I've raised the cell lenght in the z direction and added a peptide, > solvate, ionized and minimized. The next ntv step was also fine but, when I > run the npt simulation, suddenly the cell broadens in xy directions and > shrinks in z direction. > > What can be wrong with it? > > My npt.mpd file is attached. > > Thanks for your help! > > Marco FRANZOI > PhD Student > University of Padua > Department of biology, V floor South > Tel: 3405086908 > Mail: marco.franzo...@gmail.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] Vesicle simulation crashed with dry martini force field
Why do you think that it's the domain decomposition load balancing causing the crash rather than the time-step? You say you ran successfully on less CPU cores with shorter time-step. What about less cores with 10 fs time-step? It would help if you share a less mis-formatted information or even a full log file. -- Szilárd On Fri, Jan 15, 2016 at 10:12 PM, Shule Liu wrote: > Hi, > I'm trying to simulate a large lipid vesicle ( ~ 100 nm in diameter) with > the dry martini force field. The system consists of about 1.4 million > particles. I'm trying to equilibrate the system in NVT ensemble in a > simulation box with length 120 nm, using the timestep of 10 fs. The > simulation was running on 144 cores (6 nodes with 24 cores in each node). > Below is my .mdp input file. > define = -DPOSRES -DPOSRES_FC=1000 > -DBILAYER_LIPIDHEAD_FC=200integrator = sdtinit > = 0.0dt = 0.01nsteps = 800 > nstxout = 10nstvout = 1nstfout >= 1nstlog = 10nstenergy > = 1nstxtcout= 1000xtc_precision= 100 > nstlist = 10ns_type = gridpbc >= xyzrlist= 1.4 > epsilon_r= 15coulombtype = Shiftrcoulomb > = 1.2vdw_type = Shiftrvdw_switch = > 0.9rvdw = 1.2DispCorr = No > tc-grps = systemtau_t= 4.0ref_t > = 295 > ; Pressure coupling:Pcoupl = no > ; GENERATE VELOCITIES FOR STARTUP RUN:;gen_vel = > yes;gen_temp = 295;gen_seed = > 1452274742refcoord_scaling = allcutoff-scheme= group > The simulation crashed with the following error message. > Step 6105820:Atom 164932 moved more than the distance allowed by the > domain decomposition (4.00) in direction Zdistance out of cell > 127480.656250Old coordinates: 38.785 21.966 103.077New coordinates: > -477239.938 16192.882 127588.617Old cell boundaries in direction Z: > 60.580 107.937New cell boundaries in direction Z: 60.632 107.958 > ---Program mdrun_mpi, > VERSION 5.0.4Source code file: > /scratch/build/git/chemistry-roll/BUILD/sdsc-gromacs-5.0.4/gromacs-5.0.4/src/gromacs/mdlib/domdec.c, > line: 4390 > Fatal error:An atom moved too far between two domain decomposition > stepsThis usually means that your system is not well equilibratedFor more > information and tips for troubleshooting, please check the GROMACSwebsite > at > http://www.gromacs.org/Documentation/Errors--- > Error on rank 58, will try to stop all ranksHalting parallel program > mdrun_mpi on CPU 58 out of 144 > gcq#25: "This Puke Stinks Like Beer" (LIVE) > [cli_58]: aborting job:application called MPI_Abort(MPI_COMM_WORLD, -1) - > process 58 > I think my simulation crashed possibly due to the large load imbalance > generated by the domain decomposition. My system (lipid vesicle with > implicit solvent) is highly inhomogeneous, therefore the domain > decomposition algorithm will generate highly inhomogeneous domains with > some domains empty and some full of particles. I tried to run the > simulation with less CPUs (96 cores) and smaller timestep (1 fs) and there > wasn't any problem for over 6 million steps. > However, I would still like to use more cores and large timestep to > equilibrate my system. Is there any better way to control the load balance > and domain decomposition such that I could equilibrate the system more > efficiently? The dry martini paper said for such kind of vesicle > simulations domain decomposition scheme should be chosen carefully. Is > there a guidance for doing so? > Thanks very much. > Shule > -- > 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] Vesicle simulation crashed with dry martini force field
Hi, I'm trying to simulate a large lipid vesicle ( ~ 100 nm in diameter) with the dry martini force field. The system consists of about 1.4 million particles. I'm trying to equilibrate the system in NVT ensemble in a simulation box with length 120 nm, using the timestep of 10 fs. The simulation was running on 144 cores (6 nodes with 24 cores in each node). Below is my .mdp input file. define = -DPOSRES -DPOSRES_FC=1000 -DBILAYER_LIPIDHEAD_FC=200integrator = sdtinit = 0.0dt = 0.01nsteps = 800 nstxout = 10nstvout = 1nstfout = 1nstlog = 10nstenergy = 1nstxtcout = 1000xtc_precision = 100 nstlist = 10ns_type = gridpbc = xyzrlist = 1.4 epsilon_r = 15coulombtype = Shiftrcoulomb = 1.2vdw_type = Shiftrvdw_switch = 0.9rvdw = 1.2DispCorr = No tc-grps = systemtau_t = 4.0ref_t = 295 ; Pressure coupling:Pcoupl = no ; GENERATE VELOCITIES FOR STARTUP RUN:;gen_vel = yes;gen_temp = 295;gen_seed = 1452274742refcoord_scaling = allcutoff-scheme = group The simulation crashed with the following error message. Step 6105820:Atom 164932 moved more than the distance allowed by the domain decomposition (4.00) in direction Zdistance out of cell 127480.656250Old coordinates: 38.785 21.966 103.077New coordinates: -477239.938 16192.882 127588.617Old cell boundaries in direction Z: 60.580 107.937New cell boundaries in direction Z: 60.632 107.958 ---Program mdrun_mpi, VERSION 5.0.4Source code file: /scratch/build/git/chemistry-roll/BUILD/sdsc-gromacs-5.0.4/gromacs-5.0.4/src/gromacs/mdlib/domdec.c, line: 4390 Fatal error:An atom moved too far between two domain decomposition stepsThis usually means that your system is not well equilibratedFor more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors--- Error on rank 58, will try to stop all ranksHalting parallel program mdrun_mpi on CPU 58 out of 144 gcq#25: "This Puke Stinks Like Beer" (LIVE) [cli_58]: aborting job:application called MPI_Abort(MPI_COMM_WORLD, -1) - process 58 I think my simulation crashed possibly due to the large load imbalance generated by the domain decomposition. My system (lipid vesicle with implicit solvent) is highly inhomogeneous, therefore the domain decomposition algorithm will generate highly inhomogeneous domains with some domains empty and some full of particles. I tried to run the simulation with less CPUs (96 cores) and smaller timestep (1 fs) and there wasn't any problem for over 6 million steps. However, I would still like to use more cores and large timestep to equilibrate my system. Is there any better way to control the load balance and domain decomposition such that I could equilibrate the system more efficiently? The dry martini paper said for such kind of vesicle simulations domain decomposition scheme should be chosen carefully. Is there a guidance for doing so? Thanks very much. Shule -- 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] Constraining positions according to B-factors
Hi Irem, I think it would be better to actually build and simulate a crystal and use the b-factors as a result of the model that allows you to do the comparison with the diffraction data. Applying position restraints to reproduce the b-factors will yield an unphysical system, from which I think little meaningful can be deduced. But yes, kJ/mol/nm^2 Cheers, Tsjerk On Jan 15, 2016 16:57, "Irem Altan" wrote: > Hi, > > Thank you for your answer, I will try that. I realize it’s unphysical, but > I want to compare certain properties of the protein to diffraction data. > Just to double check: the values in [position_restraints] are in units of > kJ/(mol*nm^2), right? > > Best, > Irem > > > On Jan 15, 2016, at 9:47 AM, Tsjerk Wassenaar wrote: > > > > Hi Irem, > > > > Okay. First remove all bonded and nonbonded interactions, because these > are > > what gives rise to the thermal fluctuations in a real crystal. So you > would > > only need an [ atoms ] section and a section with [ position_restraints > ]. > > You should be able to calculate a spring constants based on the > > experimental b-factors. Then, if you perform the simulation and calculate > > the b-factors, you should be able to reproduce what you put in. > > > > But seriously, why would you want that? There is no force in nature that > > keeps atoms pinned to some xyz coordinate in space. What you see as > thermal > > motion is the result of the constraints due to the interactions there > are. > > Of course, that means in the context the molecule is in. If you want to > > simulate b-factors in a crystal, you've gotta simulate a crystal. Using > > physics, not using artificial means to try to reproduce what you put in. > > > > Hope it helps, > > > > Tsjerk > > > > > > On Fri, Jan 15, 2016 at 3:27 PM, Irem Altan wrote: > > > >> Hi, > >> > >> Yes, assuming a harmonic potential, I want to be able to constrain atoms > >> such that their mean square displacement during the simulation will be > >> compatible with their B-factors. > >> > >> Best, > >> Irem > >> > >>> On Jan 15, 2016, at 1:32 AM, Tsjerk Wassenaar > wrote: > >>> > >>> Hey, > >>> > >>> Under the assumption that the B-factor is caused by some atom-specific > >>> force that keeps it pinned to a certain position? > >>> > >>> Cheers, > >>> > >>> Tsjerk > >>> On Jan 15, 2016 01:18, "Irem Altan" wrote: > >>> > Hi, > > I was wondering if it was possible to constrain protein atom positions > according to their B-factors, so that their RMS displacement during > the > simulation will be compatible with their B-factors. If so, could you > >> point > me towards a helpful resource? > > Best, > Irem > -- > 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. > >> > > > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > -- > > 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/Maili
[gmx-users] Membrane simulation npt problem
Good evening to everyone. I've an issue regarding a membrane simulation. I've downloaded an already equilibrated POPE/POPG membrane and, to test the system, I run an em, a 0.1 ns nvt and 1 ns npt simulation and everything was fine. Then, I've raised the cell lenght in the z direction and added a peptide, solvate, ionized and minimized. The next ntv step was also fine but, when I run the npt simulation, suddenly the cell broadens in xy directions and shrinks in z direction. What can be wrong with it? My npt.mpd file is attached. Thanks for your help! Marco FRANZOI PhD Student University of Padua Department of biology, V floor South Tel: 3405086908 Mail: marco.franzo...@gmail.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] Out of memory error for g_density and trjconv
I've run an atomistic simulation of 2048 DOPC and 65,536 waters; so ~500,000 atoms in total. I'd like to produce an electron density plot of the bilayer so I tried to use g_density but immediately got the error message: Fatal error: Not enough memory. Failed to calloc -1082130432 elements of size 4 for grps[j].nm_ind (called from file /local/software/gromacs/5.0.4/source/gromacs-5.0.4/src/gromacs/fileio/tpxio.c, line 2510) As I get the same message even if I try to analyse the last frame of the trajectory (using the -b flag), I assume the problem is the number of atoms rather than the length of the trajectory. However I'm not sure how to proceed given that I also get the same error message immediately if I try to use trjconv to, for example, strip the waters out of the trajectory. I have a couple of questions: 1) Does the error message mean that it requires 1082130432 * 4bytes (ie ~4.5GB)? If so,I'm confused why I get this message even when I'm running on a node that has 8GB per processor (256GB for a whole 32 processor node)? How much memory is it asking for? 2) Is there any way of stripping down this trajectory (other than trjconv!) as it currently stands in order to get round the memory issue or is it just a case that these simulations are effectively wasted because I can't analyse them? Thanks -- 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] Constraining positions according to B-factors
Hi, Thank you for your answer, I will try that. I realize it’s unphysical, but I want to compare certain properties of the protein to diffraction data. Just to double check: the values in [position_restraints] are in units of kJ/(mol*nm^2), right? Best, Irem > On Jan 15, 2016, at 9:47 AM, Tsjerk Wassenaar wrote: > > Hi Irem, > > Okay. First remove all bonded and nonbonded interactions, because these are > what gives rise to the thermal fluctuations in a real crystal. So you would > only need an [ atoms ] section and a section with [ position_restraints ]. > You should be able to calculate a spring constants based on the > experimental b-factors. Then, if you perform the simulation and calculate > the b-factors, you should be able to reproduce what you put in. > > But seriously, why would you want that? There is no force in nature that > keeps atoms pinned to some xyz coordinate in space. What you see as thermal > motion is the result of the constraints due to the interactions there are. > Of course, that means in the context the molecule is in. If you want to > simulate b-factors in a crystal, you've gotta simulate a crystal. Using > physics, not using artificial means to try to reproduce what you put in. > > Hope it helps, > > Tsjerk > > > On Fri, Jan 15, 2016 at 3:27 PM, Irem Altan wrote: > >> Hi, >> >> Yes, assuming a harmonic potential, I want to be able to constrain atoms >> such that their mean square displacement during the simulation will be >> compatible with their B-factors. >> >> Best, >> Irem >> >>> On Jan 15, 2016, at 1:32 AM, Tsjerk Wassenaar wrote: >>> >>> Hey, >>> >>> Under the assumption that the B-factor is caused by some atom-specific >>> force that keeps it pinned to a certain position? >>> >>> Cheers, >>> >>> Tsjerk >>> On Jan 15, 2016 01:18, "Irem Altan" wrote: >>> Hi, I was wondering if it was possible to constrain protein atom positions according to their B-factors, so that their RMS displacement during the simulation will be compatible with their B-factors. If so, could you >> point me towards a helpful resource? Best, Irem -- 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. >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > 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] Constraining positions according to B-factors
Hi Irem, Okay. First remove all bonded and nonbonded interactions, because these are what gives rise to the thermal fluctuations in a real crystal. So you would only need an [ atoms ] section and a section with [ position_restraints ]. You should be able to calculate a spring constants based on the experimental b-factors. Then, if you perform the simulation and calculate the b-factors, you should be able to reproduce what you put in. But seriously, why would you want that? There is no force in nature that keeps atoms pinned to some xyz coordinate in space. What you see as thermal motion is the result of the constraints due to the interactions there are. Of course, that means in the context the molecule is in. If you want to simulate b-factors in a crystal, you've gotta simulate a crystal. Using physics, not using artificial means to try to reproduce what you put in. Hope it helps, Tsjerk On Fri, Jan 15, 2016 at 3:27 PM, Irem Altan wrote: > Hi, > > Yes, assuming a harmonic potential, I want to be able to constrain atoms > such that their mean square displacement during the simulation will be > compatible with their B-factors. > > Best, > Irem > > > On Jan 15, 2016, at 1:32 AM, Tsjerk Wassenaar wrote: > > > > Hey, > > > > Under the assumption that the B-factor is caused by some atom-specific > > force that keeps it pinned to a certain position? > > > > Cheers, > > > > Tsjerk > > On Jan 15, 2016 01:18, "Irem Altan" wrote: > > > >> Hi, > >> > >> I was wondering if it was possible to constrain protein atom positions > >> according to their B-factors, so that their RMS displacement during the > >> simulation will be compatible with their B-factors. If so, could you > point > >> me towards a helpful resource? > >> > >> Best, > >> Irem > >> -- > >> 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. > -- Tsjerk A. Wassenaar, Ph.D. -- 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] Launch hybrid MPI/openMP run on multiple nodes
Hi, Thus you should find out how your system administrators intended you to use the resources. Mark On Fri, 15 Jan 2016 15:01 Szilárd Páll wrote: > Hi, > > Your job scheduler and/or MPI launcher is most likely to blame. The fact > that mdrun warns about the logical core (hardware thread) mismatch means > that the OpenMP runtime thinks that you should be using one thread per > rank. This typically means that the MPI launcher or job scheduler set an > affinity mask for each rank and likely mdrun also skipped pinning threads > because of this. > > This should however alone not cause nodes to be empty, but rather it would > cause ranks to overlap and run on the same core. > > In any case, you should pass the correct ranks/node threads/rank settigns > to your launchers; to ensure correct rank placement you'll have to either > set up affinities through the scheduler or let mdrun do it. > > Cheers, > -- > Szilárd > > On Fri, Jan 15, 2016 at 9:25 AM, Chunlei ZHANG > > wrote: > > > Dear GMX developers and users, > > > > I have a cluster of 24 nodes, each having two 10-core intel CPUs. > > Gromacs 5.1 is compiled by using intel mpi (version 5.1.1) and mkl. > > > > I can successfully run a simulation by using pure MPI (480 MPI > processes). > > But the performance is not good and the log file of mdrun suggests using > > fewer MPI processes. > > I try to launch 240 MPI processes, each using 2 openMP threads, by the > > command: > > mpirun -ppn 20 -np 240 gmx_mpi mdrun -ntomp 2 > > > > But only a fraction of the nodes are running mdrun and the log file says: > > > > Number of logical cores detected (20) does not match the number reported > by > > OpenMP (1). > > Consider setting the launch configuration manually! > > > > Does anyone know how to solve this problem? > > Thanks in advance. > > > > Best, > > Chunlei > > -- > > 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] Constraining positions according to B-factors
Hi, Yes, assuming a harmonic potential, I want to be able to constrain atoms such that their mean square displacement during the simulation will be compatible with their B-factors. Best, Irem > On Jan 15, 2016, at 1:32 AM, Tsjerk Wassenaar wrote: > > Hey, > > Under the assumption that the B-factor is caused by some atom-specific > force that keeps it pinned to a certain position? > > Cheers, > > Tsjerk > On Jan 15, 2016 01:18, "Irem Altan" wrote: > >> Hi, >> >> I was wondering if it was possible to constrain protein atom positions >> according to their B-factors, so that their RMS displacement during the >> simulation will be compatible with their B-factors. If so, could you point >> me towards a helpful resource? >> >> Best, >> Irem >> -- >> 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] how to maintain planarity of graphene sheet
I checked. They are from AMBER. On Fri, Jan 15, 2016 at 5:50 AM, jagannath mondal wrote: > Hi Vitaly > > Unfortunately, the paper does not mention anything about whether the > forcefields for graphene were taken from OPLS or AMBER. > If I could get the topology file (even for part of) the graphene , it > would have been very helpful. I could have replicated and improvised the > topology files for the graphene size I am interested in. > Jagannath > > On Fri, Jan 15, 2016 at 6:14 AM, VITALY V. CHABAN > wrote: > >> The force constants were either from OPLS or from AMBER (which of these is >> referenced in the paper?) >> >> >> >> On Thu, Jan 14, 2016 at 5:40 PM, jagannath mondal >> wrote: >> >> > Hi Vitaly >> > Thanks for pointing to the paper. >> > Based on the paper, "GR was simulated as a non-polarizable assembly of >> > carbon atoms linked by harmonic potentials with the following bonded >> > parameters: distance (C–C)= 1.41 nm, angle (C–C–C) = 120 , dihedral >> (C–C–C >> > –C) =0 " >> > Can you please specify what were the values of force-constant used for >> > bonds, angle and dihedrals ? >> > Jagannath >> > >> > >> > >> > On Thu, Jan 14, 2016 at 6:53 PM, VITALY V. CHABAN >> > wrote: >> > >> >> By using high force constants for all bonded terms. >> >> >> >> An ideally planar graphene in the solution/dispersion is an unphysical >> >> model though. You must read literature for further insights: >> >> >> >> >> >> >> http://pubs.rsc.org/en/content/articlelanding/2015/ra/c5ra16857k#!divAbstract >> >> >> >> >> >> >> >> >> >> >> >> >> >> On Thu, Jan 14, 2016 at 5:13 AM, jagannath mondal > > >> >> wrote: >> >> >> >> > Hi >> >> > >> >> > Which restraints can one use to maintain planarity of graphene >> sheets >> >> > while performing MD simulations of their association ? I guess >> >> > flat-bottommed restraints will not work. >> >> > >> >> > Jagannath >> >> > -- >> >> > 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] Launch hybrid MPI/openMP run on multiple nodes
Hi, Your job scheduler and/or MPI launcher is most likely to blame. The fact that mdrun warns about the logical core (hardware thread) mismatch means that the OpenMP runtime thinks that you should be using one thread per rank. This typically means that the MPI launcher or job scheduler set an affinity mask for each rank and likely mdrun also skipped pinning threads because of this. This should however alone not cause nodes to be empty, but rather it would cause ranks to overlap and run on the same core. In any case, you should pass the correct ranks/node threads/rank settigns to your launchers; to ensure correct rank placement you'll have to either set up affinities through the scheduler or let mdrun do it. Cheers, -- Szilárd On Fri, Jan 15, 2016 at 9:25 AM, Chunlei ZHANG wrote: > Dear GMX developers and users, > > I have a cluster of 24 nodes, each having two 10-core intel CPUs. > Gromacs 5.1 is compiled by using intel mpi (version 5.1.1) and mkl. > > I can successfully run a simulation by using pure MPI (480 MPI processes). > But the performance is not good and the log file of mdrun suggests using > fewer MPI processes. > I try to launch 240 MPI processes, each using 2 openMP threads, by the > command: > mpirun -ppn 20 -np 240 gmx_mpi mdrun -ntomp 2 > > But only a fraction of the nodes are running mdrun and the log file says: > > Number of logical cores detected (20) does not match the number reported by > OpenMP (1). > Consider setting the launch configuration manually! > > Does anyone know how to solve this problem? > Thanks in advance. > > Best, > Chunlei > -- > 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] Electric field unit
Seems rational! Thank you very much David. On Thu, Jan 14, 2016 at 7:20 PM, mah maz wrote: > Thank you David but it still seems conflicting to me. V/nm and V/m are 100 > times different! If it is in V/nm then force unit should be wrong! > > On Thu, Jan 14, 2016 at 12:20 PM, mah maz wrote: > >> Hi David, >> >> In the manual 4.6.7, Page8. It seems logical since the force unit is in >> KJ/mol.nm. And it can roughly be deduced from ions movements. >> What is the use of FIELDFAC in src code then? >> >> thank you. >> >> On Thu, Jan 14, 2016 at 10:54 AM, mah maz wrote: >> >>> Dear users, >>> >>> What is the electric field unit in gromacs? In the manual it is KJ/mol. >>> nm.e but in the source code I encountered V/nm which is about 100 times >>> KJ/mol.nm.e. >>> >>> 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.
[gmx-users] Launch hybrid MPI/openMP run on multiple nodes
Dear GMX developers and users, I have a cluster of 24 nodes, each having two 10-core intel CPUs. Gromacs 5.1 is compiled by using intel mpi (version 5.1.1) and mkl. I can successfully run a simulation by using pure MPI (480 MPI processes). But the performance is not good and the log file of mdrun suggests using fewer MPI processes. I try to launch 240 MPI processes, each using 2 openMP threads, by the command: mpirun -ppn 20 -np 240 gmx_mpi mdrun -ntomp 2 But only a fraction of the nodes are running mdrun and the log file says: Number of logical cores detected (20) does not match the number reported by OpenMP (1). Consider setting the launch configuration manually! Does anyone know how to solve this problem? Thanks in advance. Best, Chunlei -- 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.
