[gmx-users] Re: Chain separation problem

[csreddy at ncbs.res.in]

Dear Periole,
Thank you so much for your kind reply, as you suggested I will keep the
discussion on the users list. Please note that I AM GETTING PROBLEM ONLY
WHEN I AM NOT USING ANY BOX.
    When I am keeping the protein in the box with or with out solution
chains are not separating.
    What I understood from your suggestion is solution for the chain
separation in the box.


Regards
Chandu


> 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.
>
> 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
> -----------------------------------------------------
>


--------------------------------------------------
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
--------------------------------------------------