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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- application/octet-stream attachment: f-m.3.pdb
Received on Tue Nov 30 2010 - 22:00:02 PST
