Re: [gmx-users] MPI error in gromacs 4.6
Hello Ankita You have to just include the following line in your mdp file cutoff-scheme=Verlet And run your grompp with the modfied mdp file to generate tpr file and then mdrun. Hope this doesn't give you the same error On Mon, Mar 24, 2014 at 4:47 PM, Ankita Naithani ankitanaith...@gmail.comwrote: Hi, I am trying to run a simulation of my protein (monomer ~500 residues). I had few questions and erors regarding the same. I have previously run the simulation of the apo form of the same protein using Gromacs 4.5.5 which was available at the cluster facility I was using and also which is installed in my system. However, when I tried to run the holo form, I got error : Fatal error: 11 particles communicated to PME node 106 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This I figured out could be solved using a lower timestep as my previous timestep was 4fs and now I have reduced it to 3fs which should work fine now. However, after producing the tpr file for production run in my GROMACS 4.5.5, I realised that the grant for the cluster facility is over and the new clusters which I am trying to set up the same protein for support only gromacs 4.6. I am trying to run the code in these clusters and I get he following error: --- Program mdrun_mpi, VERSION 4.6.3 Source code file: /home/gromacs-4.6.3/src/kernel/runner .c, line: 824 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors - 1. I wanted help with my mdp options to make it compatible. 2. Since my pevious calculations were based on gromacs 4.5.5, switching to gromacs 4.6, would that break the continuity of the run or would that bring about differences in the way the trajectories would be analysed? Below, is my mdp file title= production MD ; Run parameters integrator= md; leap-frog algorithm nsteps= ; 0.003 * = 10 ps or 100 n dt= 0.003; 3 fs ; Output control nstxout= 0; save coordinates every 2 ps nstvout= 0; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 5 ps nstenergy= 1000; save energies every 5 ps nstlog= 1000; update log file every 5 ps energygrps = Protein ATP ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT nstcomm = 10; remove com every 10 steps ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 318 318; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = berendsen; Berendsen thermostat pcoupltype= isotropic; uniform scaling of box vectors tau_p= 1.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; Velocity generation is on gen_temp= 318; reference temperature, for protein in K Kind regards-- Ankita Naithani -- 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
Re: [gmx-users] MPI error in gromacs 4.6
Hi Pavan, Thank you for your response. I am trying to generate the tpr file with the following parameter; ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) cutoff-scheme = Verlet But, I get a warning of Unknown left-hand 'cutoff-scheme' in parameter file. On Mon, Mar 24, 2014 at 11:26 AM, Pavan Kumar kumar.pavan...@gmail.comwrote: Hello Ankita You have to just include the following line in your mdp file cutoff-scheme=Verlet And run your grompp with the modfied mdp file to generate tpr file and then mdrun. Hope this doesn't give you the same error On Mon, Mar 24, 2014 at 4:47 PM, Ankita Naithani ankitanaith...@gmail.comwrote: Hi, I am trying to run a simulation of my protein (monomer ~500 residues). I had few questions and erors regarding the same. I have previously run the simulation of the apo form of the same protein using Gromacs 4.5.5 which was available at the cluster facility I was using and also which is installed in my system. However, when I tried to run the holo form, I got error : Fatal error: 11 particles communicated to PME node 106 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This I figured out could be solved using a lower timestep as my previous timestep was 4fs and now I have reduced it to 3fs which should work fine now. However, after producing the tpr file for production run in my GROMACS 4.5.5, I realised that the grant for the cluster facility is over and the new clusters which I am trying to set up the same protein for support only gromacs 4.6. I am trying to run the code in these clusters and I get he following error: --- Program mdrun_mpi, VERSION 4.6.3 Source code file: /home/gromacs-4.6.3/src/kernel/runner .c, line: 824 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors - 1. I wanted help with my mdp options to make it compatible. 2. Since my pevious calculations were based on gromacs 4.5.5, switching to gromacs 4.6, would that break the continuity of the run or would that bring about differences in the way the trajectories would be analysed? Below, is my mdp file title= production MD ; Run parameters integrator= md; leap-frog algorithm nsteps= ; 0.003 * = 10 ps or 100 n dt= 0.003; 3 fs ; Output control nstxout= 0; save coordinates every 2 ps nstvout= 0; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 5 ps nstenergy= 1000; save energies every 5 ps nstlog= 1000; update log file every 5 ps energygrps = Protein ATP ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT nstcomm = 10; remove com every 10 steps ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 318 318; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = berendsen; Berendsen thermostat
Re: [gmx-users] MPI error in gromacs 4.6
It might be some typographical errors. Check the mdp file thoroughly. I think semicolon is required for the last line in your mdp file On Mon, Mar 24, 2014 at 5:18 PM, Ankita Naithani ankitanaith...@gmail.comwrote: Hi Pavan, Thank you for your response. I am trying to generate the tpr file with the following parameter; ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) cutoff-scheme = Verlet But, I get a warning of Unknown left-hand 'cutoff-scheme' in parameter file. On Mon, Mar 24, 2014 at 11:26 AM, Pavan Kumar kumar.pavan...@gmail.com wrote: Hello Ankita You have to just include the following line in your mdp file cutoff-scheme=Verlet And run your grompp with the modfied mdp file to generate tpr file and then mdrun. Hope this doesn't give you the same error On Mon, Mar 24, 2014 at 4:47 PM, Ankita Naithani ankitanaith...@gmail.comwrote: Hi, I am trying to run a simulation of my protein (monomer ~500 residues). I had few questions and erors regarding the same. I have previously run the simulation of the apo form of the same protein using Gromacs 4.5.5 which was available at the cluster facility I was using and also which is installed in my system. However, when I tried to run the holo form, I got error : Fatal error: 11 particles communicated to PME node 106 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This I figured out could be solved using a lower timestep as my previous timestep was 4fs and now I have reduced it to 3fs which should work fine now. However, after producing the tpr file for production run in my GROMACS 4.5.5, I realised that the grant for the cluster facility is over and the new clusters which I am trying to set up the same protein for support only gromacs 4.6. I am trying to run the code in these clusters and I get he following error: --- Program mdrun_mpi, VERSION 4.6.3 Source code file: /home/gromacs-4.6.3/src/kernel/runner .c, line: 824 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors - 1. I wanted help with my mdp options to make it compatible. 2. Since my pevious calculations were based on gromacs 4.5.5, switching to gromacs 4.6, would that break the continuity of the run or would that bring about differences in the way the trajectories would be analysed? Below, is my mdp file title= production MD ; Run parameters integrator= md; leap-frog algorithm nsteps= ; 0.003 * = 10 ps or 100 n dt= 0.003; 3 fs ; Output control nstxout= 0; save coordinates every 2 ps nstvout= 0; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 5 ps nstenergy= 1000; save energies every 5 ps nstlog= 1000; update log file every 5 ps energygrps = Protein ATP ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT nstcomm = 10; remove com every 10 steps ; Temperature coupling is on tcoupl= V-rescale;
Re: [gmx-users] MPI error in gromacs 4.6
On Mon, Mar 24, 2014 at 12:17 PM, Ankita Naithani ankitanaith...@gmail.comwrote: Hi, I am trying to run a simulation of my protein (monomer ~500 residues). I had few questions and erors regarding the same. I have previously run the simulation of the apo form of the same protein using Gromacs 4.5.5 which was available at the cluster facility I was using and also which is installed in my system. However, when I tried to run the holo form, I got error : Fatal error: 11 particles communicated to PME node 106 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This I figured out could be solved using a lower timestep as my previous timestep was 4fs and now I have reduced it to 3fs which should work fine now. You should need to do that kind of thing only for equilibration, e.g. see http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation However, after producing the tpr file for production run in my GROMACS 4.5.5, I realised that the grant for the cluster facility is over and the new clusters which I am trying to set up the same protein for support only gromacs 4.6. I am trying to run the code in these clusters and I get he following error: --- Program mdrun_mpi, VERSION 4.6.3 Source code file: /home/gromacs-4.6.3/src/kernel/runner .c, line: 824 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors - 1. I wanted help with my mdp options to make it compatible. If you want to run with the group scheme, use cutoff-scheme = group, control your job script to use an MPI rank per core, and do not attempt to use OpenMP. 2. Since my pevious calculations were based on gromacs 4.5.5, switching to gromacs 4.6, would that break the continuity of the run or would that bring about differences in the way the trajectories would be analysed? Many things are different, but if you're confident no relevant bugs were fixed, you can use 4.6.x to do the same things as 4.5.5 could do. But since such runs would not have http://www.gromacs.org/Documentation/Terminology/Reproducibility, then they will not have continuity either. Below, is my mdp file title= production MD ; Run parameters integrator= md; leap-frog algorithm nsteps= ; 0.003 * = 10 ps or 100 n dt= 0.003; 3 fs ; Output control nstxout= 0; save coordinates every 2 ps nstvout= 0; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 5 ps nstenergy= 1000; save energies every 5 ps nstlog= 1000; update log file every 5 ps energygrps = Protein ATP ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT nstcomm = 10; remove com every 10 steps ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 318 318; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = berendsen; Berendsen thermostat pcoupltype= isotropic; uniform scaling of box vectors tau_p= 1.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity
Re: [gmx-users] MPI error in gromacs 4.6
On Mon, Mar 24, 2014 at 12:48 PM, Ankita Naithani ankitanaith...@gmail.comwrote: Hi Pavan, Thank you for your response. I am trying to generate the tpr file with the following parameter; ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) cutoff-scheme = Verlet But, I get a warning of Unknown left-hand 'cutoff-scheme' in parameter file. If you want to prepare a run for GROMACS 4.6, use a 4.6 version of grompp! Mark On Mon, Mar 24, 2014 at 11:26 AM, Pavan Kumar kumar.pavan...@gmail.com wrote: Hello Ankita You have to just include the following line in your mdp file cutoff-scheme=Verlet And run your grompp with the modfied mdp file to generate tpr file and then mdrun. Hope this doesn't give you the same error On Mon, Mar 24, 2014 at 4:47 PM, Ankita Naithani ankitanaith...@gmail.comwrote: Hi, I am trying to run a simulation of my protein (monomer ~500 residues). I had few questions and erors regarding the same. I have previously run the simulation of the apo form of the same protein using Gromacs 4.5.5 which was available at the cluster facility I was using and also which is installed in my system. However, when I tried to run the holo form, I got error : Fatal error: 11 particles communicated to PME node 106 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This I figured out could be solved using a lower timestep as my previous timestep was 4fs and now I have reduced it to 3fs which should work fine now. However, after producing the tpr file for production run in my GROMACS 4.5.5, I realised that the grant for the cluster facility is over and the new clusters which I am trying to set up the same protein for support only gromacs 4.6. I am trying to run the code in these clusters and I get he following error: --- Program mdrun_mpi, VERSION 4.6.3 Source code file: /home/gromacs-4.6.3/src/kernel/runner .c, line: 824 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors - 1. I wanted help with my mdp options to make it compatible. 2. Since my pevious calculations were based on gromacs 4.5.5, switching to gromacs 4.6, would that break the continuity of the run or would that bring about differences in the way the trajectories would be analysed? Below, is my mdp file title= production MD ; Run parameters integrator= md; leap-frog algorithm nsteps= ; 0.003 * = 10 ps or 100 n dt= 0.003; 3 fs ; Output control nstxout= 0; save coordinates every 2 ps nstvout= 0; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 5 ps nstenergy= 1000; save energies every 5 ps nstlog= 1000; update log file every 5 ps energygrps = Protein ATP ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT nstcomm = 10; remove com every 10 steps ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps=
Re: [gmx-users] MPI error in gromacs 4.6
On 3/24/14, 7:48 AM, Ankita Naithani wrote: Hi Pavan, Thank you for your response. I am trying to generate the tpr file with the following parameter; ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) cutoff-scheme = Verlet But, I get a warning of Unknown left-hand 'cutoff-scheme' in parameter file. That option was introduced in version 4.6. It won't work with an earlier version. -Justin On Mon, Mar 24, 2014 at 11:26 AM, Pavan Kumar kumar.pavan...@gmail.comwrote: Hello Ankita You have to just include the following line in your mdp file cutoff-scheme=Verlet And run your grompp with the modfied mdp file to generate tpr file and then mdrun. Hope this doesn't give you the same error On Mon, Mar 24, 2014 at 4:47 PM, Ankita Naithani ankitanaith...@gmail.comwrote: Hi, I am trying to run a simulation of my protein (monomer ~500 residues). I had few questions and erors regarding the same. I have previously run the simulation of the apo form of the same protein using Gromacs 4.5.5 which was available at the cluster facility I was using and also which is installed in my system. However, when I tried to run the holo form, I got error : Fatal error: 11 particles communicated to PME node 106 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This I figured out could be solved using a lower timestep as my previous timestep was 4fs and now I have reduced it to 3fs which should work fine now. However, after producing the tpr file for production run in my GROMACS 4.5.5, I realised that the grant for the cluster facility is over and the new clusters which I am trying to set up the same protein for support only gromacs 4.6. I am trying to run the code in these clusters and I get he following error: --- Program mdrun_mpi, VERSION 4.6.3 Source code file: /home/gromacs-4.6.3/src/kernel/runner .c, line: 824 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors - 1. I wanted help with my mdp options to make it compatible. 2. Since my pevious calculations were based on gromacs 4.5.5, switching to gromacs 4.6, would that break the continuity of the run or would that bring about differences in the way the trajectories would be analysed? Below, is my mdp file title= production MD ; Run parameters integrator= md; leap-frog algorithm nsteps= ; 0.003 * = 10 ps or 100 n dt= 0.003; 3 fs ; Output control nstxout= 0; save coordinates every 2 ps nstvout= 0; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 5 ps nstenergy= 1000; save energies every 5 ps nstlog= 1000; update log file every 5 ps energygrps = Protein ATP ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT nstcomm = 10; remove com every 10 steps ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 318 318; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = berendsen; Berendsen thermostat pcoupltype=
Re: [gmx-users] MPI error in gromacs 4.6, more Errors
On 3/24/14, 7:57 AM, Ankita Naithani wrote: Hi, so I modified my mdp file which now looks like the following: title= production MD ; Run parameters integrator= md; leap-frog algorithm ;nsteps= 2000; 0.005 * 2000 = 10 ps or 100 ns ;nsteps= 20; 0.005 * 20 = 1 ns ;dt= 0.005; 5 fs nsteps= ; 0.003 * = 10 ps or 100 n dt= 0.003; 3 fs ; Output control nstxout= 0; save coordinates every 2 ps nstvout= 0; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 5 ps nstenergy= 1000; save energies every 5 ps nstlog= 1000; update log file every 5 ps ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) cutoff-scheme = Verlet ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT nstcomm = 10; remove com every 10 steps ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 318 318; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = berendsen; Berendsen thermostat pcoupltype= isotropic; uniform scaling of box vectors tau_p= 1.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; Velocity generation is on gen_temp= 318; reference temperature, for protein in K -- But, when I try to generate the tpr file on the cluster itself using gromacs 4.6.3, I get the following error: NOTE 1 [file md3.mdp]: With Verlet lists the optimal nstlist is = 10, with GPUs = 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file md3.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy Generated 3403 of the 3403 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3403 of the 3403 1-4 parameter combinations Segmentation fault Can anyone please suggest further? Do as the notes suggest. They're not fatal errors, they're just cautionary. You should probably educate yourself a bit further on what all of these algorithms are by taking a look at http://www.gromacs.org/Documentation/Cut-off_schemes. The Verlet scheme is not mandatory, but it is required by the type of parallelization you requested. Reviewers may question the changes in version and cutoff methods when critiquing your work, so be aware of that. Also, the instability you are seeing is probably a result of the large time step, unless you are using virtual sites. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- 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] MPI error in gromacs 4.6, more Errors
The segmentation fault is highly unusual, and suggests that the installation of gromacs used a shared library that has now migrated/changed/whatever. I suggest you discuss that with your system admins and ask them to re-install, or re-run the GROMACS regression tests, to check things are OK. Mark On Mon, Mar 24, 2014 at 2:13 PM, Ankita Naithani ankitanaith...@gmail.comwrote: Hi Justin, Thank you very much for your reply. I shall try to work my way around and see. Kind regards, Ankita On Mon, Mar 24, 2014 at 12:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/24/14, 7:57 AM, Ankita Naithani wrote: Hi, so I modified my mdp file which now looks like the following: title= production MD ; Run parameters integrator= md; leap-frog algorithm ;nsteps= 2000; 0.005 * 2000 = 10 ps or 100 ns ;nsteps= 20; 0.005 * 20 = 1 ns ;dt= 0.005; 5 fs nsteps= ; 0.003 * = 10 ps or 100 n dt= 0.003; 3 fs ; Output control nstxout= 0; save coordinates every 2 ps nstvout= 0; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 5 ps nstenergy= 1000; save energies every 5 ps nstlog= 1000; update log file every 5 ps ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) cutoff-scheme = Verlet ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT nstcomm = 10; remove com every 10 steps ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 318 318; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = berendsen; Berendsen thermostat pcoupltype= isotropic; uniform scaling of box vectors tau_p= 1.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; Velocity generation is on gen_temp= 318; reference temperature, for protein in K -- But, when I try to generate the tpr file on the cluster itself using gromacs 4.6.3, I get the following error: NOTE 1 [file md3.mdp]: With Verlet lists the optimal nstlist is = 10, with GPUs = 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file md3.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy Generated 3403 of the 3403 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3403 of the 3403 1-4 parameter combinations Segmentation fault Can anyone please suggest further? Do as the notes suggest. They're not fatal errors, they're just cautionary. You should probably educate yourself a bit further on what all of these algorithms are by taking a look at http://www.gromacs.org/ Documentation/Cut-off_schemes. The Verlet scheme is not mandatory, but it is required by the type of parallelization you requested. Reviewers may question the changes in version and cutoff methods when critiquing your work, so be aware of that. Also, the instability you are seeing is probably a result of the large time step, unless you are using virtual sites. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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
