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

[David van der Spoel]

On Thu, 2004-12-02 at 16:57 +0800, Choon Peng wrote:
> Dear David,
> 
>    Is that really so?
Of course, the protein will diffuse. People have even estimated that
from simulations..

> Then I better stick back to using only Linear and then
> have separate views: one with protein rotating but buried waters are in
> it and the other with only backbones and fitted to remove rotations.
> We're very much concerned that our simulations are physical.
> 
It should be enough to remove linear for the entire system of protein in
solvent. The only exception is for long membrane simulations where you
might want to do linear on membrane and water separately, or for vacuum
simulations.


> Regards,
> Choon-Peng
> 
> On 12/2/04 4:07 PM, "David van der Spoel" <spoel at xray.bmc.uu.se> wrote:
> 
> > 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
> >>>> 
> >>> 
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> >> 
> >> 
> >> 
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-- 
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
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