[AMBER] regarding IWRAP in Sander

From: aneesh cna <aneeshcna.gmail.com>
Date: Sat, 31 Jul 2010 01:50:23 -0400

Dear Amber users,

                   I have two questions related to the usage of ' IWRAP '
tag in Sander.

1. Does this IWRAP has anything do with the energetics of the system?. I am
running a system with position restraint ( 1 kcal/mol ) of few molecules.
When i run the system with IWRAP=1, restraint energy shoot up to a very high
value which leads to instability of system. But when I used IWRAP=0,
system is running fine.

2. In another case, a system with protein in organic solvent, protein is
flying out of the box when IWRAP = 1. But the system seems to be running
fine with IWRAP =0.

Thanks in advance

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Received on Fri Jul 30 2010 - 23:00:03 PDT
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