On Fri, 27 Jun 2008 13:28:18 +0200
"Tsjerk Wassenaar" <[EMAIL PROTECTED]> wrote:
Hi,
That doesn't necessarily "fix" the "problem".
It is even worst! Removing the center of mass motion of your protein
alone as suggested is an aberration and should never be done!
Which position of the
protein is taken as a reference depends on the position of the first
atom. Gromacs wants to have the first atom of a molecule in the
rectangular unit cell at the origin. Even if you set comm removal for
the group, the initial orientation and/or conformational changes may
cause the first atom to jump over the boundaries.
Whatever the case, everyone doing MD simulations should be aware of
periodic boundary conditions. There is no "outside of the box".
Tsjerk
On Fri, Jun 27, 2008 at 12:58 PM, Vitaly Chaban <[EMAIL PROTECTED]> wrote:
am new to Gromacs. I tried a 10 ps simulation with a protein and after the
run, the protein came out of the box.. is it good or bad?
Its terrible. If it runs away you'll never have a new such frolicsome
protein... ;)
How can I keep the protein in the box?
Just fix it. In .mdp file write comm-grps = _YOUR_PROTEIN_GROUP_
--
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svobody sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
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