[gmx-users] Problem with removing COM translation

[Alexandre Suman de Araujo]

Em 13-08-2010 14:24, ms escreveu:
> On 12/08/10 15:25, Alexandre Suman de Araujo wrote:
>> I'm simulating a system composed by a protein centered in a sphere of
>> water in vacuum.
>>
>> The water molecules are kept within a virtual sphere with position
>> restrains between oxygen atom and a dummy atom fixed at the center of
>> the sphere. The protein can move without any restriction.
>>
>> To prevent the separation between protein and the water globule, I
>> defined "comm_grps = Protein Non-Protein" in my .mdp file (I've also
>> used the same groups in temperature coupling as suggested in GMX
>> manual). However, when I run the simulation the protein COM moves away
>> from the center (where it is in the beginning of the simulation) of the
>> water sphere. The movement of COM of the water sphere is small (less
>> than 1 angstron). For simulations of 5ns this translation is about 2
>> angstrons and for a 14 ns simulation it is more than 10 angstrons.
>>
>> Does anyone could help me with this issue?
>>
>> As far as I know, the remove of COM motion is made by subtracting the
>> COM velocity from the velocity of the atoms within the groups defined in
>> comm_grps. Is it possible to really "freeze" the movement of the COM of
>> some groups in GROMACS to achieve an absolute static COM?
>>
>> Cheers
>>
>
> I am just curious but... why are you doing actually all of this 
> instead of using a normal periodic solvent box?

The idea is to have less water molecules and, consequently, faster 
simulations.

>
> cheers,
> m.


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Alexandre Suman de Araujo                                    *
Faculdade de Ciências Farmacêuticas de Ribeirão Preto        *
Universidade de São Paulo                                    *
Dep. de Física e Química                                     *
Grupo de Física Biológica     * e-mail: asaraujo at fcfrp.usp.br*
Av. do Café, s/n°             * e-mail: ale.suman at gmail.com  *
CEP: 14040-903                * Phone: +55 (16) 3602-4172    *
Ribeirão Preto, SP, Brasil    * Phone: +55 (16) 3602-4222    *
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