Hi, I take the following steps to perform rdf calculation for my organic molecule.
min, min2, eql, eql2 and prd. In order to check, whether my molecule is intact, I generate .pdb of the entire system after each step. Till eql step, my molecule remains intact. After eql2, the molecule breaks. I make use of the following code for eql : integrator = md dt = 0.002 ; 2 fs nsteps = 500000 ; 1.0 ns nstenergy = 200 nstlog = 2000 nstxout-compressed = 10000 continuation = yes constraint-algorithm = lincs constraints = h-bonds cutoff-scheme = Verlet coulombtype = PME rcoulomb = 1.0 vdwtype = Cut-off rvdw = 1.0 DispCorr = EnerPres tcoupl = Nose-Hoover tc-grps = LIG Water tau-t = 2.0 2.0 ref-t = 298.15 298.15 nhchainlength = 1 pcoupl = Parrinello-Rahman tau_p = 2.0 compressibility = 4.46e-5 ref_p = 1.0 How to fix it? Thanks, Neha -- 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.
