[gmx-users] the protein drifts when molecular dynanic simulation
abil4616 at yahoo.co.uk
Wed Dec 1 23:38:07 CET 2004
about comm-mode = Angular
--- Choon Peng <cpchng at bii.a-star.edu.sg> wrote:
> This will remove overall rotation and translation of
> a protein.
> You'll get a warning that this works only for a
> single molecule.
how serious is this warning? can we actually use
comm-mode = angular for a protein-in-water system,
where some of the protein molecules are positionally
restrained and some are free?
> Mr Choon-Peng CHNG
> Research Associate
> Computational Biology Group
> Bioinformatics Institute, A*STAR
> 30 Biopolis Street, Level 7. Singapore 138671.
> DID: +65 6478 8301 FAX: +65 6478 9047
> WWW: http://www.bii.a-star.edu.sg/~cpchng
> On 11/30/04 9:15 PM, "Florian Haberl"
> <Florian.Haberl at chemie.uni-erlangen.de> wrote:
> > Hi
> > On Tuesday 30 November 2004 13:39, zjim wrote:
> >> Dear gmx-user
> >> When perform protein md in a box with, the
> protein drifts to one side of
> >> the box,and as the md ends(6 ns),some of it even
> comes out the box,this
> >> maybe a problem. so my quesition is why is the
> protein drift when
> >> simulation and how to avoid this. Somebody maybe
> help me
> >> thank you in advance
> > perhaps you got same prob i got:
> > should help you
> > Greetings,
> > Florian
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