[gmx-users] RE: Protein is moving out of box.

[Xavier Periole]

On Fri, 27 Jun 2008 13:28:18 +0200
  "Tsjerk Wassenaar" <tsjerkw at gmail.com> 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 <vvchaban at gmail.com> 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: chaban at univer.kharkov.ua
>> 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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