Hello all, can someone give me a hint, please? Do you need more information? Has anyone had a similar problem.
I really need to figure that out, because I will simulate other systems which can be run only with user tables. Anja - > ----- Original Message ----- > ----- Original Message ----- > From Anja Kuhnhold <anja.kuhnh...@physik.uni-halle.de> > Date Wed, 06 Jun 2012 15:07:40 +0200 > To gmx-users@gromacs.org > Subject [gmx-users] energy conservation: shift vs shifted user potential > 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
