[gmx-users] Two doubts about GMX!

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Jun 6 13:59:05 CEST 2006

Hi Samuel,

Actually 10 000 atoms (~1000 residues) doesn't sound too bad, although it
depends on the resources you have at your disposal. If the overall structure
is not expected to change much, you can try to decrease the number of
explicit solvent molecules by using an NDLP (Bekker e.a. JCC 25:1037(2004))
simulation cell. It should be possible to obtain one at
http://md.chem.rug.nl/ndlp/ Otherwise, you can mail me off list and I can
make you one if you want. Depending on the shape of your protein I expect it
to be something in between 50k to 100k atoms in total.

Best regards,


On 6/6/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Samuel Silva Pita wrote:
> > Hi, GMXers,
> > i've some doubts about the use of GMX and implicit solvent models.
> >  I have an huge system ( moreless 10 000 protein atoms) and trying to do
> MD using explicit solvents but my computer limitations doesn't work very
> well.
> > 1) someone could help me giving some light in how can i simulate my
> system in vacuum? I tried and my protein colapses using PME and GMX FF
> number 4 in GMX3.2.1;
> Find a force field parameterized for vacuum simulations, or just use a
> random number generator.
> > 2) and so, if someone have tried to incorporate implicit solvents in
> simulations like GB, SASA, or others . This would be useful for me if give
> me some instructions.
> > sincerely,
> Not in GROMACS. Try AMBER, or doubtless others.
> Mark
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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