[gmx-users] Problem with removing COM translation

ms devicerandom at gmail.com
Fri Aug 13 19:24:20 CEST 2010

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?


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