[gmx-users] Energy drift problem
feenstra at chem.vu.nl
Thu Jul 22 09:17:39 CEST 2004
xzp02 at mails.tsinghua.edu.cn wrote:
> Dear All:
> I ran a simulation for 5ns, no cut-off for VDW interaction, but finally I
> found my system(1200 atoms) have a total energy drift of 60kJ/mol! I think it's
> quite large. How large is the tolenrance typically? and which parameter can cause
60kJ drift on a total energy of 13000kJ over 10ns sounds pretty fine to me.
> I have read some posts before, and found that nstlist and vdw switch/shift can
> cause this, but I have a 1ps test, with no VDW cut-off, nstlist = 1and 10 give
> exactly the same total energy, but VDW cut-off may take into some not very large
Some issues to consider:
1) timestep in relation to dynamics of the system. for 'protein/water' like systems,
2 fs is fine, but 1 fs will give you better energy conservation.
(See: J. Comput. Chem. 20 (8), pp 786-798, 1999)
2) cut-off. You have none for VDW (does that mean you don't use PBC as well?).
If you have charged atoms, you need to consider coulomb treatment, e.g. PME
will also give you energy drift. (P.S. without cut-offs the value of nstlist
becomes irrelevant as well - as you have already seen.)
3) precision of the code. Single is fine for nearly all applications, but will
cause considerable energy drift. E.g, for my JCC paper (above) I had to use
double precision to produce the drift vs. timestep plots.
For most of these things it holds that if it is really important, you have to
check, e.g. by making a 'drift vs dt' plot. Note, that energy drift in principle
is a diffusive process, so you should average the drift over several independent
simulations if you want to determine it accurately. (There is also a discussion
on this issue in my JCC paper - there is a link to the pdf reprint on my homepage
> In the output of g_energy, which is the unit of Drift, kJ/mol? and is there
> some critical value for it?
kJ/mol/ps. There isn't really a 'hard' critical value - that depends on the type
of system you simulate and what you want to do with it.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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