Be aware that SHAKE can often fail during minimization.
A well-minimized structure should have bond lengths
very close to the reference values, unless there is some
other problem with the conformation.
Carlos
----- Original Message -----
From: "Yong Duan" <yduan_at_udel.edu>
To: <amber_at_heimdal.compchem.ucsf.edu>; "'Lich Nguyen'"
<nguyenthanhlich_at_yahoo.com>
Sent: Wednesday, November 27, 2002 1:42 PM
Subject: RE: Please help. Energy suddenly increase. Protein jump out
>
> 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).
>
> yong
>
> -----Original Message-----
> From: David A. Case [mailto:case_at_scripps.edu]
> Sent: Wednesday, November 27, 2002 11:27 AM
> To: Lich Nguyen
> Cc: amber_at_heimdal.compchem.ucsf.edu
> 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 large...you 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: case_at_scripps.edu
> 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:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================
>
>
Received on Wed Nov 27 2002 - 13:35:15 PST
