Hi All, I am working on a system of polymers having both positive and negative charge. I am using OPLS AA force field to wokr on it.
While I Vacuum simulated a single chain of the same Charged polymer without any query. After being able to do that I proceeded to Vacuum simulation using 5 chains of the same chain. keeping them at close proximities. The resultant NVT Run was very unexpected, as I visualised the nvt.gro file using VMD, the chains were all broken and far part. And was not at all recognisable. Please help me with this. This is the NVT.mdp file used for the purpose: ; Run parameters integrator = md ; leap-frog integrator nsteps = 5000000 ; 2 * 50000 = 100 ps dt = 0.001 ; 2 fs comm-mode = ANGULAR ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-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 = simple ; search neighboring grid cells cutoff-scheme = group nstlist = 0 ; 10 fs rlist = 0.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 0.0 ; short-range electrostatic cutoff (in nm) rvdw = 0.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = Cutoff ; Particle Mesh Ewald for long-range electrostatics pme_order = 0 ; cubic interpolation fourierspacing = 0.0 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = GEL; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 310 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = no ; 3-D PBC Also My main motive is to see the behaviour of the polymer in water. For that I am initially simulating them in vacuum and then plan to solvate the system with water.. Please let me know if it is the correct way. Karpurmanjari -- 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.