Hi, all, I did many simulations with Gromacs on CO2 Water mixtures on my workstation with 8 cores in parallel, the results are pretty good.
For bigger simulations, I turned to the BlueGene machine. The problem is that with exactly the same configuration files and same number of MPI tasks( 8 here) , I always got the following problems. 1773 1774 step 6870: Water molecule starting at atom 1375 can not be settled. 1775 Check for bad contacts and/or reduce the timestep if appropriate. 1776 Wrote pdb files with previous and current coordinates 1777 1778 Step 6871, time 6.871 (ps) LINCS WARNING 1779 relative constraint deviation after LINCS: 1780 rms 0.139809, max 0.559153 (between atoms 10 and 11) 1781 bonds that rotated more than 30 degrees: 1782 atom 1 atom 2 angle previous, current, constraint length 1783 10 11 78.5 0.1210 0.1813 0.1163 1784 10 12 90.0 0.1523 0.1152 0.1163 1785 1786 step 6871: Water molecule starting at atom 4576 can not be settled. 1787 Check for bad contacts and/or reduce the timestep if appropriate. 1788 1789 step 6871: Water molecule starting at atom 5794 can not be settled. 1790 Check for bad contacts and/or reduce the timestep if appropriate. 1791 Wrote pdb files with previous and current coordinates 1792 Wrote pdb files with previous and current coordinates 1793 1794 ------------------------------------------------------- 1795 Program mdrun_bgp_d, VERSION 4.5.5 1796 Source code file: pme.c, line: 538 1797 1798 Fatal error: 1799 3 particles communicated to PME node 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. 1800 This usually means that your system is not well equilibrated. 1801 For more information and tips for troubleshooting, please check the GROMACS 1802 website at http://www.gromacs.org/Documentation/Errors When I do the energy minimization or the NVT equilibration, Gromacs worked pretty well. The problem happened when I turned to the NPT equilibration. The pressure and temperature were set to be 100bar and 318K respectively. When during the NPT equlibration, the temperature and pressure keep increasing before the program halt. 1161 1162 DD step 6499 load imb.: force 6.9% 1163 1164 Step Time Lambda 1165 6500 6.50000 0.00000 1166 1167 Energies (kJ/mol) 1168 Angle LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 1169 4.50025e+01 2.21540e+04 -7.02187e+02 -1.23033e+05 -1.27743e+04 1170 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) 1171 -1.14310e+05 1.50736e+04 -9.92368e+04 3.74677e+02 -3.36430e+02 1172 Pressure (bar) Constr. rmsd 1173 1.53825e+03 1.53151e-06 1174 1175 DD step 6599 load imb.: force 5.1% 1176 1177 Step Time Lambda 1178 6600 6.60000 0.00000 1179 1180 Energies (kJ/mol) 1181 Angle LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 1182 5.41207e+01 2.32123e+04 -7.01221e+02 -1.23852e+05 -1.27349e+04 1183 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) 1184 -1.14022e+05 1.50532e+04 -9.89688e+04 3.82147e+02 -3.35505e+02 1185 Pressure (bar) Constr. rmsd 1186 2.37940e+03 1.40409e-06 1187 1188 DD step 6699 load imb.: force 4.8% 1189 1190 Step Time Lambda 1191 6700 6.70000 0.00000 1192 1193 Energies (kJ/mol) 1194 Angle LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 1195 4.70219e+01 2.37867e+04 -6.99910e+02 -1.24021e+05 -1.26862e+04 1196 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) 1197 -1.13574e+05 1.54884e+04 -9.80852e+04 4.03537e+02 -3.34252e+02 1198 Pressure (bar) Constr. rmsd 1199 3.01172e+03 1.56366e-06 1200 1201 DD step 6799 load imb.: force 6.7% 1202 1203 Step Time Lambda 1204 6800 6.80000 0.00000 1205 1206 Energies (kJ/mol) 1207 Angle LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 1208 3.79031e+01 2.70730e+04 -6.97586e+02 -1.24088e+05 -1.24549e+04 1209 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) 1210 -1.10129e+05 3.49837e+04 -7.51454e+04 1.00845e+03 -3.32036e+02 1211 Pressure (bar) Constr. rmsd 1212 9.09741e+03 3.89773e-06 The input file for the NPT equilibration is as follows. define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator ; integrator = md-vv ; leap-frog integrator nsteps = 100000 ; 2 * 50000 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps ; ; no nstxtcout nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = yes ; <--- Restarting after NVT 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 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm) ; rcoulomb = 1.5 ; short-range electrostatic cutoff (in nm) rvdw = 0.9 ; 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 ; tcoupl = nose-hoover ; modified Berendsen thermostat ; tc-grps = CO2 SOL ; two coupling groups - more accurate tc-grps = System ; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 318 ; reference temperature, one for each group, in K ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; ; turning on pressure coupling ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; ; <-- Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 100.0 ; 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 = no ; <-- Velocity generation is off ; ; I do not know what to do. This is really kind of the worst things can happen. I can not understand why it work on the workstation while can not work on the BlueGene machine. The thing is a little urgent now. If I could not go over the problem, my project will be dead. Any suggestions will be much appreciated. Thank you very much. Best Regards, Kai -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
