[gmx-users] Segmentation fault after warning regarding Listed nonbonded interaction
Hi everybody, I am trying to make a simulation of an enzyme containing a metal ion using a dummy model for it. I have inserted all the parameters, generated the topology, solvated the system, without any problem. When I try to run a first equilibration, I get the following warning: WARNING: Listed nonbonded interaction between particles 127 and 134* at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. *These particles are close to the dummy model for the metal. I believe the problem might be related to that, but I had no problem in generating topologies, or anything like that. After that warning, I have a Segmentation fault. Here is my mdp file for the test equilibration that I was trying: define = -DPOSRES -DPOSRES_WATER ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.001 ; 1 fs ; Output control nstxout = 500 ; save coordinates every 1.0 ps nstvout = 500 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps ; Bond parameters continuation= no; first dynamics run ; constraint_algorithm = lincs ; holonomic constraints constraints = none ; all bonds (even heavy atom-H bonds) constrained ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 30; 20 fs, largely irrelevant with Verlet rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals 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 ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 1 1 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 1; temperature for Maxwell distribution gen_seed= -1; generate a random seed Any clue about what is going on? Cheers, 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] Segmentation fault after warning regarding Listed nonbonded interaction
Hey Alex, I was also having the same error from two days although my topology files and mdp files were (I think) correct. Just two hours ago I corrected the problem. I just changed the timestep from 0.002 to 0.0002 and it worked. You can also try this. Regards, Vivek Sinha On Fri, Jul 18, 2014 at 12:42 AM, Alexandre Barrozo barrozo...@gmail.com wrote: Hi everybody, I am trying to make a simulation of an enzyme containing a metal ion using a dummy model for it. I have inserted all the parameters, generated the topology, solvated the system, without any problem. When I try to run a first equilibration, I get the following warning: WARNING: Listed nonbonded interaction between particles 127 and 134* at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. *These particles are close to the dummy model for the metal. I believe the problem might be related to that, but I had no problem in generating topologies, or anything like that. After that warning, I have a Segmentation fault. Here is my mdp file for the test equilibration that I was trying: define = -DPOSRES -DPOSRES_WATER ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.001 ; 1 fs ; Output control nstxout = 500 ; save coordinates every 1.0 ps nstvout = 500 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps ; Bond parameters continuation= no; first dynamics run ; constraint_algorithm = lincs ; holonomic constraints constraints = none ; all bonds (even heavy atom-H bonds) constrained ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 30; 20 fs, largely irrelevant with Verlet rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals 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 ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 1 1 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 1; temperature for Maxwell distribution gen_seed= -1; generate a random seed Any clue about what is going on? Cheers, 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.
Re: [gmx-users] Segmentation fault after warning regarding Listed nonbonded interaction
Hey Vivek, Thanks for the suggestion. I tried this, but I still get the same problem. Cheers, Alex 2014-07-17 17:58 GMT+02:00 vivek sinha viveksinha20...@gmail.com: Hey Alex, I was also having the same error from two days although my topology files and mdp files were (I think) correct. Just two hours ago I corrected the problem. I just changed the timestep from 0.002 to 0.0002 and it worked. You can also try this. Regards, Vivek Sinha On Fri, Jul 18, 2014 at 12:42 AM, Alexandre Barrozo barrozo...@gmail.com wrote: Hi everybody, I am trying to make a simulation of an enzyme containing a metal ion using a dummy model for it. I have inserted all the parameters, generated the topology, solvated the system, without any problem. When I try to run a first equilibration, I get the following warning: WARNING: Listed nonbonded interaction between particles 127 and 134* at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. *These particles are close to the dummy model for the metal. I believe the problem might be related to that, but I had no problem in generating topologies, or anything like that. After that warning, I have a Segmentation fault. Here is my mdp file for the test equilibration that I was trying: define = -DPOSRES -DPOSRES_WATER ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.001 ; 1 fs ; Output control nstxout = 500 ; save coordinates every 1.0 ps nstvout = 500 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps ; Bond parameters continuation= no; first dynamics run ; constraint_algorithm = lincs ; holonomic constraints constraints = none ; all bonds (even heavy atom-H bonds) constrained ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 30; 20 fs, largely irrelevant with Verlet rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals 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 ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 1 1 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 1; temperature for Maxwell distribution gen_seed= -1; generate a random seed Any clue about what is going on? Cheers, 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
Re: [gmx-users] Segmentation fault after warning regarding Listed nonbonded interaction
On 7/17/14, 1:18 PM, Alexandre Barrozo wrote: Hey Vivek, Thanks for the suggestion. I tried this, but I still get the same problem. Reducing the timestep is just a band-aid for the underlying problems. Sometimes it can be useful in initial preparation for very sensitive systems, but in this case I think it is clear that the topology is not sane. -Justin Cheers, Alex 2014-07-17 17:58 GMT+02:00 vivek sinha viveksinha20...@gmail.com: Hey Alex, I was also having the same error from two days although my topology files and mdp files were (I think) correct. Just two hours ago I corrected the problem. I just changed the timestep from 0.002 to 0.0002 and it worked. You can also try this. Regards, Vivek Sinha On Fri, Jul 18, 2014 at 12:42 AM, Alexandre Barrozo barrozo...@gmail.com wrote: Hi everybody, I am trying to make a simulation of an enzyme containing a metal ion using a dummy model for it. I have inserted all the parameters, generated the topology, solvated the system, without any problem. When I try to run a first equilibration, I get the following warning: WARNING: Listed nonbonded interaction between particles 127 and 134* at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. *These particles are close to the dummy model for the metal. I believe the problem might be related to that, but I had no problem in generating topologies, or anything like that. After that warning, I have a Segmentation fault. Here is my mdp file for the test equilibration that I was trying: define = -DPOSRES -DPOSRES_WATER ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.001 ; 1 fs ; Output control nstxout = 500 ; save coordinates every 1.0 ps nstvout = 500 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps ; Bond parameters continuation= no; first dynamics run ; constraint_algorithm = lincs ; holonomic constraints constraints = none ; all bonds (even heavy atom-H bonds) constrained ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 30; 20 fs, largely irrelevant with Verlet rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals 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 ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 1 1 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 1; temperature for Maxwell distribution gen_seed= -1; generate a random seed Any clue about what is going on? Cheers, 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
