----- Original Message -----
----- Original Message -----
From Mark Abraham<[email protected]>
Date Sat, 09 Jun 2012 12:59:17 +1000
To Discussion list for GROMACS users<[email protected]>
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: [email protected]
Datum: Freitag, Juni 8, 2012 15:55
Betreff: gmx-users Digest, Vol 98, Issue 52
An: [email protected]
----- Ursprüngliche Nachricht -----
Von Mark Abraham<[email protected]>
Datum Fri, 08 Jun 2012 23:40:35 +1000
An Discussion list for GROMACS users<[email protected]>
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<[email protected]>
Date Wed, 06 Jun 2012 15:07:40 +0200
To [email protected]
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
