Hello All, I have been having rather bizarre experience with Gromacs and was wondering if any one can shed some light on what is happening. I am running simulations of a hydrate + water system (think of hydrate as ice if you are not familiar with them). So basically I have a simple solid+liquid system. The system is minimized. The water model I am using is TIP4P/2005. Now when I run the simulation using grompp and mdrun both from Gromacs 4.5.5, my system crashes and writes out step*.pdb files. This I know happens when the system is exploding or something however, I do not see an obvious reason for this. However, if I compile the tpr file with older Gromacs version 4.0.5 and then use mdrun from 4.5.5 to run the simulation, my simulation proceeds just fine....the way I expect it to.
Can anyone tell me what might be happening here. I have pasted my mdp file below. I think this might be related to the constraint algorithm but I have no idea how to fix it. I have tried using Lincs instead of Shake and that also gives the same outcome. Runs with Gromacs 4.0.5 (i.e. grompp using 4.0.5 and mdrun using 4.5.5) and fails with 4.5.5 (both grompp and mdrun using 4.5.5). Please let me know if you need any further information and thanks a lot for your help. Any insight will be helpful. #### BEGIN MDP FILE ####### title = s1-Hydrate melting simulation dt = 0.002 ; time step nsteps = 5000 ; number of steps nstcomm = 10 ; reset c.o.m. motion nstxout = 7500 ; write coords nstvout = 7500 ; write velocities nstlog = 25000 ; print to logfile nstenergy = 250 ; print energies xtc_grps = System nstxtcout = 25 nstlist = 10 ; update pairlist ns_type = grid ; pairlist method coulombtype = PME rvdw = 1.20 ; cut-off for vdw rcoulomb = 1.20 ; cut-off for coulomb rlist = 1.20 ; cut-off for coulomb Tcoupl = Nose-Hoover ref_t = 200.0 tc-grps = System tau_t = 0.5 Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic ; pressure geometry tau_p = 1.0 1.0 ; p-coupoling time compressibility = 4.5e-5 4.5e-5 ; compressibility ref_p = 100.0 100.0 ; ref pressure DispCorr = EnerPres ; long range correction gen_vel = yes ; generate init. vel gen_temp = 200 ; init. temp. gen_seed = 98247 ; random seed constraints = hbonds ; constraining bonds with H constraint_algorithm = shake #### END MDP FILE ####### Thanks very much, Sapna -- Sapna Sarupria Assistant Professor Department of Chemical and Biomolecular Engineering 128 Earle Hall Clemson University Clemson, SC 29634 Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
