[gmx-users] Opinion: Can position restraining waters increase the speed of the md simulation?

Suman Chakrabarty suman at sscu.iisc.ernet.in
Sat Oct 11 11:18:55 CEST 2008

On a related note, I remember reading a paper recently, where they take
a few shells of water molecules with full atomicity, but "continuum"
beyond that. They also took care about the exchange between the
"molecular" water shell and the continuum as the polymer/protein
conformation changes during the simulation. I have no idea how
computationally efficient that would be though.


Tsjerk Wassenaar wrote:
> Hi Art,
> You could, but should you? What do you think to gain? One layer of
> water is approximately 2.5 A, so with 6 you'd have about two layers of
> water 'free'. With position restraints on the rest, you'd still be
> calculating all forces and such, so there's not much gain there. On
> top of that, the two water layers without position restraints will
> likely be quite 'icy', giving a severe constriction of your protein
> dynamics. Basically, your protein dynamics will be close to
> nonsensical; an undefined and unrealistic restricted ensemble. Now
> even if you're only interested in the dynamics at an active site,
> consider that such dynamics is part of the whole-scale protein
> dynamics. It's not just filling making up most of the protein.
> Cheers,
> Tsjerk
> On Fri, Oct 10, 2008 at 8:25 PM, Arthur Roberts <aroberts99163 at yahoo.com> wrote:
>>> Hi, all,
>> In a previous email, I asked about the availability of implicit water
>> calculations in Gromacs 4.0, which might be available in Gromacs 4.1.  In
>> the meantime, I was wondering if I position restrained waters that are 6
>> Angstroms from the protein, would that increase the speed of md simulation,
>> if I have a water shell that extends 15 Angstroms.  I would appreciate your
>> input.
>> Best wishes,
>> Art Roberts
>> University of Washington

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