[gmx-users] Re: Chain separation problem

Xavier Periole X.Periole at rug.nl
Mon Nov 26 11:59:18 CET 2007

On Mon, 26 Nov 2007 11:44:22 +0100
  "Xavier Periole" <X.Periole at rug.nl> wrote:
> 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.

Sorry I thought you had the problem only when using a box!
Then I am also confused. Without boundaries this should not happen.
Check you input must be something funny there.


> 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.
> XAvier
>> 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
> http://md.chem.rug.nl/~periole
> -----------------------------------------------------
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XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands

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