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?
cheers,
m.
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