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
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----- 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
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