Another option would be to use solvateoct instead of solvatebox, to
generate an octahedral box (take a look into AmberTools manual for
details). Still, you'd need to estimate the maximum size of your
system and calculate the padding from there.
Cheers,
Gustavo.
On Thu, Jul 8, 2010 at 1:15 AM, Jason Swails <jason.swails.gmail.com> wrote:
> Hello,
>
> I've put my comments below in line with your email.
>
> On Wed, Jul 7, 2010 at 10:41 PM, Logan Ahlstrom <logana.email.arizona.edu>wrote:
>
>> In regards to the issue stated below, is there any way to prevent the
>> center-of-mass (COM) rotation of a molecule during simulation? I have
>> come-across the nscm flag, but this will only remove translational COM for
>> periodic simulations. Any suggestions would be much appreciated.
>>
>
> As far as I know, there is no way of removing rotations during the
> simulation. The only way I know of doing this is to use ptraj to align the
> trajectory to a reference, the first structure, the last structure, etc.
> after the trajectory has been created.
>
>
>>
>> Sincerely,
>>
>> Logan S. Ahlstrom
>> University of Arizona
>> Department of Chemistry and Biochemistry
>> Miyashita Lab
>>
>> I am currently running an explicit water REMD simulation of a dimer that
>> roughly has the shape of a “dumbbell”. Thus, when I solvate the system by
>> simply specifying a padding distance extending from the molecular
>> dimensions, a rectangle results. However, during simulation the molecule
>> rotates such that the long side of the “dumbbell” extends along the
>> shortest
>> side of the rectangle and the protein becomes too close to its periodic
>> neighbors (i.e. within the the van der Waals and electrostatic cut-off I
>> have specified). As for now, the only way I can think to fix this problem
>> is to solvate my system in a large cube such that the length of each side
>> is
>> greater than the length of the “dumbbell” plus the cut-off distance.
>> However, this dramatically increases the number of water molecules needed
>> for simulation.
>>
>
> Even in this situation, if there was a way to remove rotational motions, it
> would seem to me that the rotational motions of the entire system (including
> water) would have to be eliminated, or you'd have, in all likelihood, van
> der waals and electrostatic clashes as the protein was rotated (wrt the
> frame of reference of the water box) onto a water molecule. Therefore, even
> if an nscm for rotations did exist, I don't think it would help much in this
> situation.
>
> Your options are, as I see them, to enlarge your box to avoid this problem,
> use implicit solvent (GB or something), or use restraints to prevent
> rotational motions, though this could be tricky. You could potentially
> place a couple "ghost atoms" that have no charge, vdw, mass, etc., but whose
> positions you fix via positional restraints. Then maybe you can constrain a
> dihedral angle between 2 atoms on either side of the dumbbell and the 2
> ghost atoms you fixed. Or maybe you'd need 2 dihedral restraints... I can't
> quite visualize it right now, but you can use geometry to help here. In any
> case, it seems like a clumsy hack that's probably not worthwhile anyway (and
> it may have other side-effects that you don't want).
>
> All the best,
> Jason
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Received on Thu Jul 08 2010 - 06:00:03 PDT
