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

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Oct 11 11:05:01 CEST 2008

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.



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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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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