[gmx-users] Can I use gromos43a1p-4.5.1.tar.gz in gromacs5.0?
Dear Gmx users, I want to simulate a protein which has phosphorelated residues. Can I use gromos43a1p-4.5.1.tar.gz in gromacs5.0 or 4.6? I have got following error: Program pdb2gmx, VERSION 4.6.5 Source code file: /build/buildd/gromacs-4.6.5/src/kernel/pgutil.c, line: 126 Fatal error: Residue 2000697817 named THR of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in an interaction of type improper in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Best regards, Batsaikhan -- 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] Segmentation fault error
*Dear all,* *I am trying to simulate a system of drug carrier consisting of HSPC/CHOL in the form of a vesicle. The code works well for the system when the CHOL molecules are not inserted. As I include CHOL molecules I face this error:* *starting mdrun 'Chol/HSPC VESICLE'90 steps, 27000.0 ps.step 0[compute-0-3:30916] *** Process received signal ***[compute-0-3:30916] Signal: Segmentation fault (11)[compute-0-3:30916] Signal code: Address not mapped (1)[compute-0-3:30916] Failing at address: 0x9a200b0[compute-0-3:30916] [ 0] /lib64/libpthread.so.0 [0x316940eb10][compute-0-3:30916] [ 1] /opt/bio/gromacs/lib/libgmx_mpi.so.6 [0x2b291ac0ee2c][compute-0-3:30916] *** End of error message ***--mpirun noticed that process rank 10 with PID 30916 on node compute-0-3.local exited on signal 11 (Segmentation fault).--* *Here is the mdp file:* *title= Martiniintegrator = mddt = 0.03 nsteps = 90nstcomm = 100comm-grps= nstxout = 1000nstvout = 1000nstfout = 1000nstlog = 1000 ; Output frequency for energies to log file nstenergy= 100 ; Output frequency for energies to energy filenstxtcout= 1000 ; Output frequency for .xtc filextc_precision= 100xtc-grps = energygrps = HSPC CHOL Wnstlist = 10ns_type = gridpbc = xyzrlist= 1.4coulombtype = Shift ;Reaction_field (for use with Verlet-pairlist) ;PME (especially with polarizable water)rcoulomb_switch = 0.0rcoulomb = 1.2epsilon_r= 15 ; 2.5 (with polarizable water)vdw_type = Shift ;cutoff (for use with Verlet-pairlist) rvdw_switch = 0.9rvdw = 1.2 ;1.1 (for use with Verlet-pairlist);cutoff-scheme= verlet;coulomb-modifier = Potential-shift;vdw-modifier = Potential-shift;epsilon_rf = 0 ; epsilon_rf = 0 really means epsilon_rf = infinity;verlet-buffer-drift = 0.005tcoupl = v-rescale tc-grps = HSPC CHOL Wtau_t= 1.0 1.0 1.0 ref_t= 323 323 323Pcoupl = berendsen ; parrinello-rahman ; parrinello-rahmanPcoupltype = isotropic ; semiisotropictau_p= 3.0; 12.0 12.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422compressibility = 3e-4 ; 3e-4ref_p= 1.0; 1.0 1.0gen_vel = yesgen_temp = 320gen_seed = 473529constraints = none constraint_algorithm = Lincscontinuation = nolincs_order = 4lincs_warnangle = 30* *I appreciate any help in advance.* -- Seyed Mojtaba Rezaei Sani Institute for Research in Fundamental Sciences (IPM) School of Nano-Science Shahid Farbin Alley Shahid Lavasani st P.O. Box 19395-5531 Tehran, Iran Tel: +98 21 2310 (3069) -- 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] Maximun time-step recommended in the grompp part for each system
Dear all, Taking look at the check_bonds_timestep() function in src/kernel/grompp.c used for checking the time-step used for the integration of the equations of motion a few questions come to me: - In the comments of the function it is said that The stability limit of leap-frog or velocity verlet is 4.44 steps per oscillational period. Does anyone know how this exact number is obtained? - I see that, inside of the function, there are two limits: 5 and 10. They are used for establishing a relation between the estimated oscillation period of the bond between two atoms of the system in use and the time-step used for integrating the equations of motion and giving a warning message in case of using a non suitable time-step. I assume, looking at the literature, that this limits are taking from the following paper by Mazur: http://www.sciencedirect.com/science/article/pii/S0021999197957405 Am I right? I have also found an issue in redmine for the function check_bonds_timestep() reporting that it only reports the first suspicious bond. I think this does not affect my questions. Thank you very much. Best regards, Mario -- 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] Morse potential for Specific Group
On Dec 10, 2014 10:21 PM, Jackson Chief Elk jchief...@gmail.com wrote: Hi, I am building my own routine to use the Gromacs API to do MS-EVB. I need to treat O-H bonds of 1 hydronium ion with a Morse Potential. How can I specify in the *.mdp file, to just describe bonding in hydronium using this potential? You can use morse=yes in the .mdp file, but this turns all bonds present in the molecular system into Morse ones. To use Morse selectively, the only solution is to put this information into the topology. Goog luck, Bogdan -- 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] xeon-phi and double precision
Hi. Does xeon-phi make double precision gromacs faster? -- 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] Segmentation fault error
*Dear all,* *I am trying to simulate a system of drug carrier consisting of HSPC/CHOL in the form of a vesicle. The code works well for the system when the CHOL molecules are not inserted. As I include CHOL molecules I face this error:* *starting mdrun 'Chol/HSPC VESICLE'90 steps, 27000.0 ps.step 0[compute-0-3:30916] *** Process received signal ***[compute-0-3:30916] Signal: Segmentation fault (11)[compute-0-3:30916] Signal code: Address not mapped (1)[compute-0-3:30916] Failing at address: 0x9a200b0[compute-0-3:30916] [ 0] /lib64/libpthread.so.0 [0x316940eb10][compute-0-3:30916] [ 1] /opt/bio/gromacs/lib/libgmx_mpi.so.6 [0x2b291ac0ee2c][compute-0-3:30916] *** End of error message ***--mpirun noticed that process rank 10 with PID 30916 on node compute-0-3.local exited on signal 11 (Segmentation fault).--* *Here is the mdp file:* *title= Martiniintegrator = mddt = 0.03 nsteps = 90nstcomm = 100comm-grps= nstxout = 1000nstvout = 1000nstfout = 1000nstlog = 1000 ; Output frequency for energies to log file nstenergy= 100 ; Output frequency for energies to energy filenstxtcout= 1000 ; Output frequency for .xtc filextc_precision= 100xtc-grps = energygrps = HSPC CHOL Wnstlist = 10ns_type = gridpbc = xyzrlist= 1.4coulombtype = Shift ;Reaction_field (for use with Verlet-pairlist) ;PME (especially with polarizable water)rcoulomb_switch = 0.0rcoulomb = 1.2epsilon_r= 15 ; 2.5 (with polarizable water)vdw_type = Shift ;cutoff (for use with Verlet-pairlist) rvdw_switch = 0.9rvdw = 1.2 ;1.1 (for use with Verlet-pairlist);cutoff-scheme= verlet;coulomb-modifier = Potential-shift;vdw-modifier = Potential-shift;epsilon_rf = 0 ; epsilon_rf = 0 really means epsilon_rf = infinity;verlet-buffer-drift = 0.005tcoupl = v-rescale tc-grps = HSPC CHOL Wtau_t= 1.0 1.0 1.0 ref_t= 323 323 323Pcoupl = berendsen ; parrinello-rahman ; parrinello-rahmanPcoupltype = isotropic ; semiisotropictau_p= 3.0; 12.0 12.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422compressibility = 3e-4 ; 3e-4ref_p= 1.0; 1.0 1.0gen_vel = yesgen_temp = 320gen_seed = 473529constraints = none constraint_algorithm = Lincscontinuation = nolincs_order = 4lincs_warnangle = 30* *I appreciate any help in advance.* -- Seyed Mojtaba Rezaei Sani Institute for Research in Fundamental Sciences (IPM) School of Nano-Science Shahid Farbin Alley Shahid Lavasani st P.O. Box 19395-5531 Tehran, Iran Tel: +98 21 2310 (3069) -- 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 error
Hi, This is a generic MPI error message. Nobody can tell from it what caused it. You need to look at the whole stdout and the mdrun .log file for diagnostics. You should also report your Gromacs version. Probably you are just http://www.gromacs.org/Documentation/Terminology/Blowing_Up, but there is a known problem with 5.0.3 which we will fix ASAP. Mark On Fri, Dec 12, 2014 at 3:55 AM, Seyed Mojtaba Rezaei Sani s.m.rezaeis...@gmail.com wrote: *Dear all,* *I am trying to simulate a system of drug carrier consisting of HSPC/CHOL in the form of a vesicle. The code works well for the system when the CHOL molecules are not inserted. As I include CHOL molecules I face this error:* *starting mdrun 'Chol/HSPC VESICLE'90 steps, 27000.0 ps.step 0[compute-0-3:30916] *** Process received signal ***[compute-0-3:30916] Signal: Segmentation fault (11)[compute-0-3:30916] Signal code: Address not mapped (1)[compute-0-3:30916] Failing at address: 0x9a200b0[compute-0-3:30916] [ 0] /lib64/libpthread.so.0 [0x316940eb10][compute-0-3:30916] [ 1] /opt/bio/gromacs/lib/libgmx_mpi.so.6 [0x2b291ac0ee2c][compute-0-3:30916] *** End of error message ***--mpirun noticed that process rank 10 with PID 30916 on node compute-0-3.local exited on signal 11 (Segmentation fault).--* *Here is the mdp file:* *title= Martiniintegrator = mddt = 0.03 nsteps = 90nstcomm = 100comm-grps= nstxout = 1000nstvout = 1000nstfout = 1000nstlog = 1000 ; Output frequency for energies to log file nstenergy= 100 ; Output frequency for energies to energy filenstxtcout= 1000 ; Output frequency for .xtc filextc_precision= 100xtc-grps = energygrps = HSPC CHOL Wnstlist = 10ns_type = gridpbc = xyzrlist= 1.4coulombtype = Shift ;Reaction_field (for use with Verlet-pairlist) ;PME (especially with polarizable water)rcoulomb_switch = 0.0rcoulomb = 1.2epsilon_r= 15 ; 2.5 (with polarizable water)vdw_type = Shift ;cutoff (for use with Verlet-pairlist) rvdw_switch = 0.9rvdw = 1.2 ;1.1 (for use with Verlet-pairlist);cutoff-scheme= verlet;coulomb-modifier = Potential-shift;vdw-modifier = Potential-shift;epsilon_rf = 0 ; epsilon_rf = 0 really means epsilon_rf = infinity;verlet-buffer-drift = 0.005tcoupl = v-rescale tc-grps = HSPC CHOL Wtau_t= 1.0 1.0 1.0 ref_t= 323 323 323Pcoupl = berendsen ; parrinello-rahman ; parrinello-rahmanPcoupltype = isotropic ; semiisotropictau_p= 3.0; 12.0 12.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422compressibility = 3e-4 ; 3e-4ref_p= 1.0; 1.0 1.0gen_vel = yesgen_temp = 320gen_seed = 473529constraints = none constraint_algorithm = Lincscontinuation = nolincs_order = 4lincs_warnangle = 30* *I appreciate any help in advance.* -- Seyed Mojtaba Rezaei Sani Institute for Research in Fundamental Sciences (IPM) School of Nano-Science Shahid Farbin Alley Shahid Lavasani st P.O. Box 19395-5531 Tehran, Iran Tel: +98 21 2310 (3069) -- 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] xeon-phi and double precision
Hi, Probably not by much. Your best bet is to talk someone else into running on it, so that you can run mdrun on the resources they'd otherwise consume. :-) Mark On Fri, Dec 12, 2014 at 3:34 AM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. Does xeon-phi make double precision gromacs faster? -- 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.
