Try setting iwrap to 0, and then reimaging with ptraj. Do you get the same
effect?
On Tue, Nov 30, 2010 at 11:58 PM, chicago.ecnu <chicago.ecnu.gmail.com>wrote:
> Dear Amber users,
>
> I run MD simulation with "iwrap=1".
> This keyword has the same function as "image" in ptraj.
> However, the structure I got from such simulation seems bad.
> Many solvent molecules were overlapped (One pdb file was attached).
> The MD simulation process works very well, the whole system didn't bomb up.
> Maybe there are some problem in the process of saving coordinate.
>
> For I want to analyze waters around special amino acids, I want to get the
> real solvent distrubution state from the trajectory.
> Is there any way I can make up?
> I have tried ptraj, but not work.
>
> Many thanks for your help.
>
> Yours Sincerely,
> Changge Ji
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>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Dec 01 2010 - 07:00:06 PST
