Dear Amber users:
I would like a quick clarification regarding flags nscm and iwrap. As I understood nscm removes rotational and translational center of mass (com) movement (and in Langevin dynamics I believe just the position of com is reset but no change in velocities). So essentially, in a long (say 100+ ns) MD simulation nscm can stop overflowing coordinate format in trajectory or restart files. Iwrap can also be used to stop overflowing coordinate format in output files by wrapping the atoms into the periodic box. However, I have a feeling that implications of nscm and iwrap flags would be different on your simulation. Could someone please tell me whether this thinking is correct or whether I'm missing something here?
Thank you,
Maal
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Received on Sat Sep 18 2010 - 05:00:03 PDT
