Ok, that didn't help me much. Of course I changed both, potential and force to shifted ones. And sure I used a little fortran code to generate the tables --
I have found the problem: I thought GROMACS would ignore the table values above the cutoff distance, but it does not. I added zeros and now it works. Thanks anyway Anja > ----- Original Message ----- > ----- Original Message ----- > From Mark Abraham <mark.abra...@anu.edu.au> > Date Sat, 09 Jun 2012 12:59:17 +1000 > To Discussion list for GROMACS users <gmx-users@gromacs.org> > Subject Re: [gmx-users] Re: Re: energy conservation: shift vs > shifted user potential > On 9/06/2012 2:05 AM, Anja Kuhnhold wrote: > > Ok, I try to explain it again :) > > I know the format of the user tables (x, f(x), -f'(x), g(x), -g'(x), > h(x), -h'(x); > > f is coulomb, g dispersion, h repulsion). > > For testing the simple cut-off version, my table looks like the > > example in the installation. > > So I run a simulation with vdwtype=cut-off > > and the same with vdwtype=user. > > The results are the same. > > > > The problem is, that I want to use shifted forces and potentials > within my tables. > > (Aim is better energy conservation) > > In the manual (ch. 4.1.5) is explained how the shift functions > > for forces and potentials have to be. > > So for -g(x) and h(x) I use the potential from the manual, Phi, with > alpha=6 and 12, respectivly. > > And for g'(x) and -h'(x) I use the shifted force from the manual, > Fs, with alpha=6 and 12, respectivly. > > But when I run the simulation with this table on the one hand > > and with vdwtype=Shift on the other hand, > > the results are not comparable, mostly the energy is not conserved > by using the table. > > The force is the negative derivative of the potential. If you change > only the force columns then you have made the interaction piecewise > discontinuous at every segment. So when GROMACS uses both the values > and > derivatives to convert your table into the internal format used > (section > 6.7.1), it comes up with junk. There should be a warning printed if > the > force column is not close enough to the numerical derivative of the > potential column, but maybe this change is close enough that you avoid > > that. Anyway, this makes energy basically impossible to conserve. You > > should generate all your table values from the actual function you > wish > to implement, e.g. with a spreadsheet or scripting language. > > Mark > > > > > Can you follow me? > > > > Anja > > > > > > > > ----- Ursprüngliche Nachricht ----- > > Von: gmx-users-requ...@gromacs.org > > Datum: Freitag, Juni 8, 2012 15:55 > > Betreff: gmx-users Digest, Vol 98, Issue 52 > > An: gmx-users@gromacs.org > > > >> ----- Ursprüngliche Nachricht ----- > >> Von Mark Abraham<mark.abra...@anu.edu.au> > >> Datum Fri, 08 Jun 2012 23:40:35 +1000 > >> An Discussion list for GROMACS users<gmx-users@gromacs.org> > >> Betreff Re: [gmx-users] Re: energy conservation: shift vs shifted user > >> potential > >> On 8/06/2012 5:59 PM, Anja Kuhnhold wrote: > >>> 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? > >> We've no real idea what you've done... manual 6.7.2 describes the > >> required format and there are (unshifted) examples in your > >> installation > >> under $GMXLIB/share/top/table*.xvg. > >> > >> Makr > >> > >>>> 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! 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