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.
Re: [gmx-users] Simulation crashed - Large VCM, Pressure scaling more than 1%, Bond length not finite
Hi, If it was something fundamentally wrong, you'd see an issue before this. Martini is just inherently a teensy bit unstable - but this is where the non-reproducibility of simulations comes in handy; restarting from far enough away will likely avoid a transiently high energy event. Kevin On Tue, Feb 26, 2019 at 4:57 AM zeineb SI CHAIB wrote: > Dear Kevin, > > Thank you for your reply. > > I did 2 tests: > 1- I wanted to see in details when the system crashes and which atoms are > involved so I restarted the simulation from the checkpoint but using a new > mdp file. The only parameter that I changed was nstxout-compressed = 1. In > this case, the simulation didn't crash. > The command lines that I used were: > gmx grompp -f md_2.mdp -c npt.gro -p topol.top -n index.ndx -o md_2.tpr > gmx mdrun -deffnm md_2 -cpi md.cpt -noappend -nt 1 > > 2- I restarted the simulation from the same checkpoint as in (1), using > the first mdp file (with nstxout-compressed = 1000) and the simulation > crashed again at the same step. > The command line that I used were: > gmx mdrun -deffnm md -cpi md.cpt -noappend -nt 1 > > I compared the log files of (1) and (2) and it's starting from the same > time/steps but as I said (1) didn't crash and (2) crashed. > > I can restart the simulation with the new mdp file and keep it running > again but I want to be sure that It's a random crash and it is not a sign > of something more fundamentally wrong (physically unrealistic) with my > system. > > Zeineb > > > -- > Gromacs Users mailing list > > * Please search the archive at > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_Listdata=02%7C01%7Ckevin.boyd%40uconn.edu%7C1f38b091b8c643b55beb08d69bd0e0b5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636867718780368928sdata=cRy2XaqophqHtri3oM1ULmutD4SkyOahI8ciWmRmdIw%3Dreserved=0 > before posting! > > * Can't post? Read > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Listsdata=02%7C01%7Ckevin.boyd%40uconn.edu%7C1f38b091b8c643b55beb08d69bd0e0b5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636867718780378938sdata=zhoh9PJa1GBu41GleQ9KQ5CKgbZeNO0X6fS0pkDnV%2F8%3Dreserved=0 > > * For (un)subscribe requests visit > > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-usersdata=02%7C01%7Ckevin.boyd%40uconn.edu%7C1f38b091b8c643b55beb08d69bd0e0b5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636867718780378938sdata=yXVlFuucw%2FqadP%2FOQKc0SLVPGBtOygkiGKZWwnEHsTI%3Dreserved=0 > 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] Simulation crashed - Large VCM, Pressure scaling more than 1%, Bond length not finite
Dear Kevin, Thank you for your reply. I did 2 tests: 1- I wanted to see in details when the system crashes and which atoms are involved so I restarted the simulation from the checkpoint but using a new mdp file. The only parameter that I changed was nstxout-compressed = 1. In this case, the simulation didn't crash. The command lines that I used were: gmx grompp -f md_2.mdp -c npt.gro -p topol.top -n index.ndx -o md_2.tpr gmx mdrun -deffnm md_2 -cpi md.cpt -noappend -nt 1 2- I restarted the simulation from the same checkpoint as in (1), using the first mdp file (with nstxout-compressed = 1000) and the simulation crashed again at the same step. The command line that I used were: gmx mdrun -deffnm md -cpi md.cpt -noappend -nt 1 I compared the log files of (1) and (2) and it's starting from the same time/steps but as I said (1) didn't crash and (2) crashed. I can restart the simulation with the new mdp file and keep it running again but I want to be sure that It's a random crash and it is not a sign of something more fundamentally wrong (physically unrealistic) with my system. 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] Simulation crashed - Large VCM, Pressure scaling more than 1%, Bond length not finite
Dear GMX users, I am running a Coarse-Grained simulation using Martini Force Field. My system consists of a Protein inserted in a lipid bilayer containing POPC, POPE, and CHOL molecules, in the presence of Water and ions. I followed the conventional steps to prepare my system for the production run: 1- Generating Coarse-Grained structure and topology files 2- Insertion of the protein in the lipid bilayer 3- Adding neutralizing counterions 4- Energy minimization with backbone positions restraints for 1ns. 5- NVT equilibration with backbone positions restraints for 50 ns with v-rescale. 6- NPT equilibration with backbone positions restraints for 50 ns with Parrinello-Rahman barostat. The simulation runs for ~ 2 microseconds before crashing: Large VCM (group Protein_POPC_POPE_CHOL): 965789.43750, -1086946.5, 135001.78125, Temp-cm: 9.21574e+14 Large VCM(group W_ION): -396609.0, 446514.28125, -55416.26953, Temp-cm: 2.38187e+13 Step 123438101 Warning: Pressure scaling more than 1%. This may mean your system is not yet equilibrated. Use of Parrinello-Rahman pressure coupling during equilibration can lead to simulation instability and is discouraged. Program: gmx mdrun, version 2018.3 Source file: src/gromacs/mdlib/clincs.cpp (line 2252) Fatal error: Bond length not finite. I used the following parameters in the mdp file (They were recommended by Martini People): integrator = md dt = 0.02 nsteps = 5 nstxout = 100 nstvout = 100 nstfout= 0 nstlog = 1000 nstenergy = 100 nstxout-compressed = 1000 compressed-x-precision = 100 continuation = yes cutoff-scheme= Verlet nstlist = 20 ns_type = grid pbc = xyz verlet-buffer-tolerance = 0.005 coulombtype= reaction-field rcoulomb = 1.1 epsilon_r = 15 epsilon_rf = 0 vdw_type = cutoff vdw-modifier = Potential-shift-verlet rvdw = 1.1 tcoupl = v-rescale tc-grps= Protein POPC_POPE_CHOL W_ION tau_t = 1.0 1.0 1.0 ref_t= 315 315 315 Pcoupl= parrinello-rahman Pcoupltype= semiisotropic tau_p = 12.0 compressibility = 3e-4 3e-4 3e-4 ref_p = 1.0 1.0 1.0 gen_vel = no gen_temp= 315 gen_seed = 473529 constraints = none constraint_algorithm = Lincs nstcomm = 100 comm-grps = Protein_POPC_POPE_CHOL W_ION I had a look on the GROMACS mailing list for similar problems and probable causes: In one post they said that the Large VCM might be related to an un-equilibrated system but in my case, the system was equilibrated for 50ns (NVT equilibration) and another 50ns for the NPT equilibration so I don't think that this is the case here. Another suggestion for the VCM thing is that it might be related to the force field and the topology. Since the last 5 residues of my protein have not been solved I thought that it's better to keep the actual C-terminal residue neutral. I would have liked to use the capping residues but they are not parameterized in Martini force field. Maybe this is why the simulation is crashing? But it runs for more than 2 microseconds before it crashed! I would like to have your opinion about this point, please. The error message is really confusing and I can't really understand it : VCM/Pressure scaling more that 1%/Bond length not finite. I would really appreciate your help on this. 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.
