Re: vlimit exceeded when sander calculate free energies using TI

From: David A. Case <>
Date: Wed, 11 Jun 2003 08:21:31 -0700

On Wed, Jun 11, 2003, zsx wrote:

> I have used the Cap water , ibelly=1 and ntb=0, it can run normally
> dynamics in sander7, but when I use the normal dynamic *.rst as the input
> file for sander7 TI calculation, icfe=1 and clambda=0.04691, the VDW energy
> and Temperature will increase uncontrolly, then break down. I want to know
> the reason, for it seem that it will go normally with period condition
> system.

There is probably some problem with your prmtop setup. The first thing you
should always do with problems like this is run a 10-20 step simulation
with ntpr=1. That way, you can see the energies and their differences in
detail. If the reported DV/DL number is big, there is something wrong with
the perturbed prmtop file. Try running short simulations at both lambda=0
and lambda=1, and see if you can identify what the problems are.

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
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Received on Wed Jun 11 2003 - 16:53:01 PDT
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