Dear Dr. Cui,
You might try ptraj (see the Amber 6.0 manual) to re-center solute and
solvent--this works for my system which is solvated with a water box
rather than a cap. (Did the problem occur during md simulation or in the
actual capping process?) In the md run, iwrap probably should be set to 1
(for a box, though I'm not sure about a cap). Good luck.
Sincerely,
Michael G. Cooney
Dept. of Biochemistry and Molecular Biology
University of Georgia
Athens, GA 30602, USA
On Wed, 25 Jul 2001, Guanglei Cui wrote:
> Dear Amber Users,
> Recently I'm trying to pick up the solvatecap command and add a small
> water cap to my system. In a few attempts, the water cap departed from
> the system substantially even though all water molecules were still
> capped with the specified sphere. What I see is that my system of
> interest is in one place but the water cap is in another. To me, it
> seems it is the cap that moved not the system itself. Could anyone show
> me how to perform MD with water caps correctly? (I simply solvatecap mol
> WATBOX216 {atom1 atom2 atom3} 12.5A and used default ivcap and fcap or
> stronger fcap) Thanks in advance.
>
> Regards,
>
> Guanglei Cui
> SUNY at Stony Brook
>
Received on Wed Jul 25 2001 - 10:27:54 PDT
