[gmx-users] Re: Chain separation problem

Xavier Periole X.Periole at rug.nl
Mon Nov 26 11:44:22 CET 2007

On Mon, 26 Nov 2007 15:33:36 +0530 (IST)
  csreddy at ncbs.res.in wrote:
> Dear Periole,
> Thank you so much for your suggestion. I was not sure weather to reply all
> or  individually. 

It is always better to keep the discussion on the users list. The info
given might serve other users.

> I am sorry I am not clear about your answer. I am
> getting the problem only when I am not using the box, but you said to
> center the protein in the box? Could you please explain this.

When you use a box the program will deal with the position of the
system relative to the box faces. If a molecule (first atom) moves
and crosses the dimension of the box on one axis (x,y,z) -it
physically gets out of the box- it will be replaced inside the box
on the opposite box-side (same axis). Have a look at the manual or
any text book on simulations, this will be more clearly explained.
When you build your system, it might be that one part of it is
inside the box and the other part is outside. This is more likely
to happen when multimeric structures are simulated. Then the program
will automatically replace the parts of the system that are outside
the box to the inside. Note that the system does not feel it.

If you want to avoid this you have to center your system before
doing any minimization. Note that the box has to be large enough
to accommodate your system plus solvent.


> Thanks in advance
> Chandu
> On Mon, 26 Nov 2007 13:45:01 +0530 (IST)
>  csreddy at ncbs.res.in wrote:
>> Hi All,
>> I have been trying run energy minimization for a homoTRIMER protein, I
>> have puzzled by the following results!
>> 1) energy minimization in vacuum 1 chain is separated from the remaining 2
>> chains. I tried for 5 models in 4 models chains are separated and one is
>> normal.
>> 2)energy minimization in box with or with out solvent, no chain separation
>> for all the 5 models.
>> please note that EM method is steepest decent, I have tried size on the
>> box up to 20nm.
> you are probably experiencing the effect of PBC. In the cases you
> see "separation", centering the protein in the box should solve the
> problem.
> --------------------------------------------------
> C.Chandra Sekhar Reddy (Research Scholar)
> Laboratoire de Biochimie et Génétique Moléculaire
> Université de La Réunion
> 15, avenue René Cassin
> 97715 Saint Denis Messag Cedex 09
> La Réunion, France
> Tel : +262 262 93 8641 MOB +262 (0)692 44 49 42
>Fax : +262 262 93 8237
> --------------------------------------------------

XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands

More information about the gromacs.org_gmx-users mailing list