mm_pbsa & nmode

From: FyD <>
Date: Tue, 08 Apr 2003 17:04:38 +0200 (CEST)

Dear All,
I use mm_pbsa to determine the entropy of MD snapshots. Thus, 'sander' is first used with
a drms = 0.0001 and then nmode is launched with a drms=0.001. During the sander
minimization, I never reach the demanded RMS (I always get a RMS between 4.10-2 & 1.10-2):
Then, I understand I get the following error when I use nmode:
Root-mean-square gradient of input coords is 1.1469293833725278E-002
This is greater than the requested maximum: 1.0000000000000000E-003
I have 2 questions:
- Do you have a way to solve this problem ?
I could use 'nmode' to optimize my molecule instead of 'sander' but I guess it is not
implemented in mm_pbsa or is it OK to simply increase the RMS. What would be the maximum
RMS value I could use to determine the entropy of the MD snapshots ?
- and why nsnb = 99999 in the sander input ?
Thanks, regards, Francois
Received on Tue Apr 08 2003 - 16:53:02 PDT
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