[gmx-users] "Floating point exception" for g_rms
Dear GROMACS experts, (Relevant files can be found on https://copy.com/7DMkn6OxJBqEZtqh) I have been told in the error file: ... ... Reading frame1700 time 17000.000 Reading frame1800 time 18000.000 Reading frame1900 time 19000.000 Reading frame2000 time 2.000 -- mpirun noticed that process rank 0 with PID 3 on node node-080 exited on signal 8 (Floating point exception). -- when I tried to submit a job with commandline below on our cluster: echo "2 2" | gerun g_rms -s md_0_1.tpr -f md_0_1.xtc Can I ask what is incorrect in my job? Thank you very much. Yours sincerely Cheng -- 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] "Floating point exception" for g_rms
On 6/20/15 7:54 AM, Zhang, Cheng wrote: Dear GROMACS experts, (Relevant files can be found on https://copy.com/7DMkn6OxJBqEZtqh) I have been told in the error file: ... ... Reading frame1700 time 17000.000 Reading frame1800 time 18000.000 Reading frame1900 time 19000.000 Reading frame2000 time 2.000 -- mpirun noticed that process rank 0 with PID 3 on node node-080 exited on signal 8 (Floating point exception). -- when I tried to submit a job with commandline below on our cluster: echo "2 2" | gerun g_rms -s md_0_1.tpr -f md_0_1.xtc Can I ask what is incorrect in my job? Thank you very much. Don't run analysis tools in parallel. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
[gmx-users] Floating point exception(core dumped) still happen when running a serial job
Dear GROMACS expert, (Relevant files can be found at https://copy.com/7DMkn6OxJBqEZtqh) I still encountered error of "Floating point exception(core dumped)" when running "g_rms -s md_0_1.tpr -f md_0_1.xtc" on my Ubuntu. In the prompt, it stopped and showed the error when it came to 20 ns: ... ... Reading frame1700 time 17000.000 Reading frame1800 time 18000.000 Reading frame1900 time 19000.000 Reading frame2000 time 2.000 However, in my another repeat simulation, it could successfully run "g_rms -s md_0_1.tpr -f md_0_1.xtc" based on another md_0_1.xtc file. So I think there is something wrong with this .xtc file. Could someone please help me identify the problem? Thank you very much. Yours sincerely Cheng -- 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] Floating point exception(core dumped) still happen when running a serial job
On 6/20/15 11:04 AM, Zhang, Cheng wrote: Dear GROMACS expert, (Relevant files can be found at https://copy.com/7DMkn6OxJBqEZtqh) I still encountered error of "Floating point exception(core dumped)" when running "g_rms -s md_0_1.tpr -f md_0_1.xtc" on my Ubuntu. In the prompt, it stopped and showed the error when it came to 20 ns: ... ... Reading frame1700 time 17000.000 Reading frame1800 time 18000.000 Reading frame1900 time 19000.000 Reading frame2000 time 2.000 However, in my another repeat simulation, it could successfully run "g_rms -s md_0_1.tpr -f md_0_1.xtc" based on another md_0_1.xtc file. So I think there is something wrong with this .xtc file. Could someone please help me identify the problem? What does gmx check tell you about the contents of the problematic .xtc file? It's probably corrupted. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
[gmx-users] “gmx check" shows "Floating point exception(core dumped)" for .xtc file
Hi Justin, Thank you for telling me the "gmx check" method. As I checked, it also shows "Floating point exception(core dumped)" after 20 ns. So I think it is corrupt as you have said. I will run it again. Thank you very much. Yours sincerely Cheng GROMACS: gmx check, VERSION 5.0.4 Executable: /usr/local/gromacs/bin/gmx Library dir: /usr/local/gromacs/share/gromacs/top Command line: gmx check -f md_0_1.xtc Reading frame 0 time0.000 # Atoms 127896 Precision 0.001 (nm) Reading frame 1 time 10.000 Reading frame 2 time 20.000 Reading frame 3 time 30.000 Reading frame 4 time 40.000 Reading frame 5 time 50.000 Reading frame 6 time 60.000 Reading frame 7 time 70.000 Reading frame 8 time 80.000 Reading frame 9 time 90.000 Reading frame 10 time 100.000 Reading frame 11 time 110.000 Reading frame 12 time 120.000 Reading frame 13 time 130.000 Reading frame 14 time 140.000 Reading frame 15 time 150.000 Reading frame 16 time 160.000 Reading frame 17 time 170.000 Reading frame 18 time 180.000 Reading frame 19 time 190.000 Reading frame 20 time 200.000 Reading frame 30 time 300.000 Reading frame 40 time 400.000 Reading frame 50 time 500.000 Reading frame 60 time 600.000 Reading frame 70 time 700.000 Reading frame 80 time 800.000 Reading frame 90 time 900.000 Reading frame 100 time 1000.000 Reading frame 110 time 1100.000 Reading frame 120 time 1200.000 Reading frame 130 time 1300.000 Reading frame 140 time 1400.000 Reading frame 150 time 1500.000 Reading frame 160 time 1600.000 Reading frame 170 time 1700.000 Reading frame 180 time 1800.000 Reading frame 190 time 1900.000 Reading frame 200 time 2000.000 Reading frame 300 time 3000.000 Reading frame 400 time 4000.000 Reading frame 500 time 5000.000 Reading frame 600 time 6000.000 Reading frame 700 time 7000.000 Reading frame 800 time 8000.000 Reading frame 900 time 9000.000 Reading frame1000 time 1.000 Reading frame1100 time 11000.000 Reading frame1200 time 12000.000 Reading frame1300 time 13000.000 Reading frame1400 time 14000.000 Reading frame1500 time 15000.000 Reading frame1600 time 16000.000 Reading frame1700 time 17000.000 Reading frame1800 time 18000.000 Reading frame1900 time 19000.000 Reading frame2000 time 2.000 -- 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] Help me with energy groups please.
For my main MD experiment, I run just the energy group System. This is fine. Then I take one configuration and run a minimization. For the minimization, I have two energy groups: peg2000 (my polymer), and Water so that I can inspect interaction energies. Here is the output from gmx energy: Energy Average Err.Est. RMSD Tot-Drift --- Morse 13.8929 1192.2316 -69.4839 (kJ/mol) G96Angle347.715 62127.946 -413.973 (kJ/mol) Proper Dih. 128.924 0.551.13049 -3.826 (kJ/mol) LJ-14 71.4762 24.16065 -13.8959 (kJ/mol) Coulomb-14 988.758 0.12 0.239868 0.836523 (kJ/mol) LJ (SR) 3263212.9 5.9749 -20.3545 (kJ/mol) Coulomb (SR) -1.85621e+06 0.360.80798 -2.48026 (kJ/mol) Coul. recip.2094.03 0.015 0.0317153 0.0976681 (kJ/mol) LJ recip. -30437.1 0.0032 0.00707587 -0.0217548 (kJ/mol) Potential-1.55669e+06 78191.241 -523.261 (kJ/mol) Pressure -2.80437e+345.7e+27 1.27529e+28 3.80388e+28 (bar) #Surf*SurfTen-1.35113e+331.8e+29 3.66158e+29 1.18298e+30 (bar nm) Coul-SR:peg2000-peg2000 -1.85621e+06 0.360.80798 -2.48026 (kJ/mol) LJ-SR:peg2000-peg20003263212.9 5.9749 -20.3545 (kJ/mol) Coul-14:peg2000-peg2000 988.758 0.12 0.239868 0.836523 (kJ/mol) LJ-14:peg2000-peg2000 71.4762 24.16065 -13.8959 (kJ/mol) Coul-SR:peg2000-Water 0 0 0 0 (kJ/mol) LJ-SR:peg2000-Water 0 0 0 0 (kJ/mol) Coul-14:peg2000-Water 0 0 0 0 (kJ/mol) LJ-14:peg2000-Water 0 0 0 0 (kJ/mol) Coul-SR:Water-Water 0 0 0 0 (kJ/mol) LJ-SR:Water-Water 0 0 0 0 (kJ/mol) Coul-14:Water-Water 0 0 0 0 (kJ/mol) LJ-14:Water-Water 0 0 0 0 (kJ/mol) ddd It appears I have no interaction energy between my polymer and the water and there is no interaction energy intra-Water. This makes no sense! I am using the standard spce water witch does have partial charges and my polymer has partial charges. There should be coulomb interaction and there should always be LJ interaction. Help me figure this out please. Attached is my mdp file. Dan Sponseller ** Run Control ** integrator = steep nsteps = 1 comm-mode= Linear nstcomm = 100 ** Energy Minimization emtol= 0.001 emstep = 0.01 ** Output Control ** nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 0 nstcalcenergy= 1 nstenergy= 1 energygrps = peg2000 Water ** Neighbor Searching ** cutoff-scheme= Verlet nstlist = 20 ns_type = grid pbc = xyz periodic-molecules = no verlet-buffer-tolerance = 0.001 ** Electrostatics ** coulombtype = PME coulomb-modifier = Potential-shift-Verlet rcoulomb = 1.5 ** VdW ** vdwtype = PME vdw-modifier = Potential-shift-Verlet rvdw = 1.5 ** Ewald ** fourierspacing = 0.15 pme-order= 6 ewald-rtol = 1e-5 ** Temperature Coupling ** tcoupl = no ;tcoupl = v-rescale nsttcouple = -1 tc-grps = System tau-t= 1.0 ref-t= 300 ** Pressure Coupling ** pcoupl = no ;pcoupl = Parrinello-Rahman ;pcoupl = Berendsen pcoupltype = isotropic nstpcouple = -1 tau-p= 2.0 compressibility = 4.5e-5 ref-p= 1 refcoord-scaling = all ** Velocity Generation ** gen-vel = no gen-temp = 300 gen-seed = 4242 ** Bonds ** constraints = none morse= yes -- 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] Help me with energy groups please.
On 6/20/15 4:48 PM, Dan Sponseller wrote: For my main MD experiment, I run just the energy group System. This is fine. Then I take one configuration and run a minimization. For the minimization, I have two energy groups: peg2000 (my polymer), and Water so that I can inspect interaction energies. Here is the output from gmx energy: Energy Average Err.Est. RMSD Tot-Drift --- Morse 13.8929 1192.2316 -69.4839 (kJ/mol) G96Angle347.715 62127.946 -413.973 (kJ/mol) Proper Dih. 128.924 0.551.13049 -3.826 (kJ/mol) LJ-14 71.4762 24.16065 -13.8959 (kJ/mol) Coulomb-14 988.758 0.12 0.239868 0.836523 (kJ/mol) LJ (SR) 3263212.9 5.9749 -20.3545 (kJ/mol) Coulomb (SR) -1.85621e+06 0.360.80798 -2.48026 (kJ/mol) Coul. recip.2094.03 0.015 0.0317153 0.0976681 (kJ/mol) LJ recip. -30437.1 0.0032 0.00707587 -0.0217548 (kJ/mol) Potential-1.55669e+06 78191.241 -523.261 (kJ/mol) Pressure -2.80437e+345.7e+27 1.27529e+28 3.80388e+28 (bar) #Surf*SurfTen-1.35113e+331.8e+29 3.66158e+29 1.18298e+30 (bar nm) Coul-SR:peg2000-peg2000 -1.85621e+06 0.360.80798 -2.48026 (kJ/mol) LJ-SR:peg2000-peg20003263212.9 5.9749 -20.3545 (kJ/mol) Coul-14:peg2000-peg2000 988.758 0.12 0.239868 0.836523 (kJ/mol) LJ-14:peg2000-peg2000 71.4762 24.16065 -13.8959 (kJ/mol) Coul-SR:peg2000-Water 0 0 0 0 (kJ/mol) LJ-SR:peg2000-Water 0 0 0 0 (kJ/mol) Coul-14:peg2000-Water 0 0 0 0 (kJ/mol) LJ-14:peg2000-Water 0 0 0 0 (kJ/mol) Coul-SR:Water-Water 0 0 0 0 (kJ/mol) LJ-SR:Water-Water 0 0 0 0 (kJ/mol) Coul-14:Water-Water 0 0 0 0 (kJ/mol) LJ-14:Water-Water 0 0 0 0 (kJ/mol) ddd It appears I have no interaction energy between my polymer and the water and there is no interaction energy intra-Water. This makes no sense! I am using the standard spce water witch does have partial charges and my polymer has partial charges. There should be coulomb interaction and there should always be LJ interaction. Help me figure this out please. Attached is my mdp file. It's probably because you're doing EM and not dynamics. Not all dynamics features are enabled in EM. That would be my first guess. Try running a quick MD with the same energygrps. If those show up correctly, you have your answer. -Justin Dan Sponseller ** Run Control ** integrator = steep nsteps = 1 comm-mode= Linear nstcomm = 100 ** Energy Minimization emtol= 0.001 emstep = 0.01 ** Output Control ** nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 0 nstcalcenergy= 1 nstenergy= 1 energygrps = peg2000 Water ** Neighbor Searching ** cutoff-scheme= Verlet nstlist = 20 ns_type = grid pbc = xyz periodic-molecules = no verlet-buffer-tolerance = 0.001 ** Electrostatics ** coulombtype = PME coulomb-modifier = Potential-shift-Verlet rcoulomb = 1.5 ** VdW ** vdwtype = PME vdw-modifier = Potential-shift-Verlet rvdw = 1.5 ** Ewald ** fourierspacing = 0.15 pme-order= 6 ewald-rtol = 1e-5 ** Temperature Coupling ** tcoupl = no ;tcoupl = v-rescale nsttcouple = -1 tc-grps = System tau-t= 1.0 ref-t= 300 ** Pressure Coupling ** pcoupl = no ;pcoupl = Parrinello-Rahman ;pcoupl = Berendsen pcoupltype = isotropic nstpcouple = -1 tau-p= 2.0 compressibility = 4.5e-5 ref-p= 1 refcoord-scaling = all ** Velocity Generation ** gen-vel = no gen-temp = 300 gen-seed = 4242 ** Bonds ** constraints = none morse= yes -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow
[gmx-users] lost particles wile sorting
Dear gromacs experts, I am using semiisotropic coupling to pull a helix along z. I defined wall like this: pbc = xy nwall= 2 wall-atomtype= CH3 CH3 wall-type= 12-6 wall-r-linpot= 1 1 wall-density = 5 5 But mdrun give me the following error: Program mdrun, VERSION 5.0.4 Source code file: /home/tm/Downloads/gromacs/src/gromacs/mdlib/nbnxn_search.c, line: 737 Software inconsistency error: Lost particles while sorting For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Then I tried to use 1 and 2 openMP threads, mdrun give me this error: step 0: Water molecule starting at atom 40708 cannot be settled. Check for bad contacts and/or reduce the time step if appropriate. Segmentation fault (core dumped) Could you please help to tell me how to fix this problem? Thanks in advance. -- 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] gas phase force field
Hello all, Can any one please tell me which force fields are used for accurate prediction of gas phases on organics? RegardsSwapnil -- 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.
