Dear Sadaf:
You are starting with lambda = 10, which appears to be a state in which VDW is off, but Coulomb is (partially) on. I’ve not used the FE code in gromacs for quite some time (since it at least used to be unexpectedly slow compared to regular simulations), but I suspect that this is your problem — with q but no VDW you can get two charged atoms getting really close and generating huge Coulombic forces, leading to system explosion. I believe that it is normal to have q completely off before you start turning off the VDW. Other thoughts, not likely related to your crashes, but I include them since I looked at your .mdp file already: why not use nstlist = 10 ? I’m not sure why nstlist = 20 is ever OK with a 2 fs time step, but I realize that gromacs has made some recent strides in NBlist building, so I might be misinformed here. I get fine sd integrator stability with lincs-order = 6. Not sure how much performance a lincs order of 12 is costing you, but you might be OK with 6 here. Your tau_t is pretty small for velocity Langevin dynamics and you may be in the over-damped regime. You may get more collective dynamics (and better overall sampling) with a 1 ps value of tau_t. Parrinello-Rahman pressure coupling, though giving a better ensemble than Berendsen, is more fragile and will lead to exploding systems more easily than Berendsen pressure coupling if your out of pressure/volume equilibrium. You might at least try using Berendsen pressure coupling and see if it fixes your issues. You have gen_vel = no. Suggest to verify that you are in fact loading in velocities. Good luck, Chris. -- 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.
