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

Thu Dec 2 13:35:12 CET 2004

true, protein diffuses, but in solution. in the solid
or semi-sloid state translational motion of protein
can be safely ignored. so its not so unphysical as it
might seem first. what i am worried about is how good
gromacs and its force fields (i am using 53a6) are for
simulations of protein+water in the solid state. 

the model itself is similar to that in water solution:
i surround 1 protein (+ its x-ray water) with many
other proteins, add more water to fill the gaps, then
positionally restrain the surrounding proteins and let
the central one evolve. this incidentally solves the
problem of protein drifting out of the box, but
creates another problem of disk space. cpuwise i didnt
notice much slow down compared to 1  protein in water.

 --- David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> 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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