[gmx-users] the protein drifts when molecular dynanic simulation

[David van der Spoel]

On Wed, 2004-12-01 at 22:38 +0000, Abil Aliev wrote:
> 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?
Yes you can, but it's unphysical. If that doesn't bother you, then, by
all means try it out.
> 
> > 
> > 
> > Regards,
> > Choon-Peng
> > -- 
> > 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:
> > > 
> > >
> >
> http://www.gromacs.org/pipermail/gmx-users/2004-November/012902.html
> > > 
> > > should help you
> > > 
> > > Greetings,
> > > 
> > > Florian
> > > 
> > 
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the
> > list. Use the 
> > www interface or send it to
> > gmx-users-request at gromacs.org.
> >  
> 
> 
> 		
> ___________________________________________________________ 
> Win a castle for NYE with your mates and Yahoo! Messenger 
> http://uk.messenger.yahoo.com
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++