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

From: Yong Duan <>
Date: Wed 27 Nov 2002 13:42:39 -0500

My guess is that you did not apply SHAKE when you minimized the
structure. If this is the case, I think you do not have to worry about
it. But if you are concerned, apply the same level of SHAKE in
minimization as the one that you will use in MD. The spike will
magically disappear (in most cases).


-----Original Message-----
From: David A. Case []
Sent: Wednesday, November 27, 2002 11:27 AM
To: Lich Nguyen
Subject: Re: Please help. Energy suddenly increase. Protein jump out

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

> &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 - 10:42:39 PST
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