Hello, I want to simulate a box of polymer (32 chains) with salt. I started with one chain of the polymer in the box. However, after the energy minimisation, the energy is still positive. I found the discussion in the link below very similar to the problem I have:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users /2017-February/111219.html and tried the tips from Justin in the link but I still get positive energy. This is my first MDP file: define = integrator = steep nsteps = -1 nstcgsteep = 10 constraints = none lincs_order = 8 emtol = 20 emstep = 0.01 comm-mode = Linear nstcomm = 1 nstcalcenergy = 1 ; Output frequency for energies to log file and energy file nstlog = 1 nstenergy = 1 ns_type = grid cutoff-scheme = verlet coulombtype = PME nstlist = 10 rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 1 pbc = xyz and this is the second one which I tried to follow the tips from the link mentioned above: define = integrator = steep nsteps = -1 nstcgsteep = 10 constraints = none lincs_order = 8 emtol = 20 emstep = 0.01 comm-mode = Linear nstcomm = 1 nstcalcenergy = 1 ; Output frequency for energies to log file and energy file nstlog = 1 nstenergy = 1 ns_type = grid cutoff-scheme = group coulombtype = cut-off nstlist = 0 rlist = 0 rcoulomb = 0 rvdw = 0 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 1 pbc = no My questions are: - I'm not sure if either of these MDP files are correct for the system I'm trying to simulate? - Why energy is positive in this simulation? Is there something fundamentally wrong in the simulation which I'm not aware of? Regards, Mahsa -- 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.