Dear gmx-users, I have a problem concerning energy conservation when using user potentials (tables). I'm using gromacs 4.5.4 I simulate a simple Lennard-Jones(6-12) +Fene polymer melt (1600 chains a 10 beads in a 26x26x26 periodic box).
I tried different vdwtypes (cutoff always 3.24): The cut-off version does not conserve energy -- okay. The shift and switch versions conserve energy -- fine. Now I wanted to do the same with user tables: Simple Lennard-Jones table gives really the same results as the cut-off version -- good. But if I use a table with shifted Lennard-Jones potential it is not comparable to the shift version and the energy is not conserved -- ? I use a shift function as written in the manual (chapter 4.1.5) -- there must be a factor alpha added in the constants A and B -- (r1=0). The parameters are the same for shift version and shifted user version. Has someone an idea why the shifted user potential doesn't work in this way? Here is the mdp: integrator = md-vv dt = 0.0035 nsteps = 1000 nstxout = 1 nstvout = 1 nstfout = 1 nstlog = 1 ns_type = grid pbc = xyz rvdw = 3.24 rlist = 3.6 tcoupl = no tc-grps = System tau_t = 2.0 ref_t = 127.2717 vdwtype = user;Shift rcoulomb = 3.6;2.24;1.12 coulombtype = Cut-off rvdw-switch = 0.0 energygrps = bead energygrp_table = bead bead Thanks in advance Anja -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
