[AMBER] entropy Calculation

From: Him Shweta <shwetahim.gmail.com>
Date: Wed, 9 Jul 2014 10:42:06 +0530

Dear all,

I am running entrop calculation in MMPBSA.py for a quadruplex-ligand
system with an input file as below:

Input file for running entropy calculations using NMode


   endframe=100, keep_files=0,



   nmstartframe=1, nmendframe=100,

   nminterval=1, maxcyc=10000, drms=0.1,
   nmode_igb=1, nmode_istrng=0.0,


Here, in this calculation when i am using convergence criteria (drms =
0.1), the result is more close to my experimental result, while with
drms=0.001, the result does not match or is closer to my experimental
The thing here which is confusing to me is, can i use a convergence
criteria for minimized energy gradient as 0.1 (drms).

Please give your input and suggestions.

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Received on Tue Jul 08 2014 - 22:30:02 PDT
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