Re: Please help. Energy suddenly increase. Protein jump out

From: David A. Case <>
Date: Wed 27 Nov 2002 08:26:55 -0800

On Tue, Nov 26, 2002, Lich Nguyen wrote:
> However, my supervisor wonders something must be wrong
> because my protein jump out at the first time step of
> simulation and both EP and EK increase suddenly.
> Time step 0: EK=0 EP=-240528 Temp=0
> 1: EK=27062 EP=-240528 Temp=223.11
> 2: EK=22866 EP=-209771 Temp=188.52
> 3: EK=13.9 EP=-209782 Temp=0.11

You are getting an enormous spike in KE on step 1. Are you sure that your
system is really minimized? Does the minimzation end at the same potential
energy has you start with the dynamics?

I note that your vdW energy on step zero is 32,000....this is not consistent
with having a minimized structure. Also, the EEL energy (-300000) is very should probably check to make sure that you don't have two
atoms very near to each other. For example, use the "checkoverlap" command in
ptraj to see if you have any obvious short distances.

> &wt type='TEMP0', istep1=0,istep2=1000,value1=0.0,
> value2=5.0, &end

Try just doing a "simple" (nmropt=0) short run with temp0=5.0. There
may be a problem with having temp0=0 on the first step.

..hope this helps...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
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Received on Wed Nov 27 2002 - 08:26:55 PST
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