Re: peptid bond omega, problems with settings?

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Thu Apr 15 2004 - 11:25:56 CDT

Just a few comments:

First, is your box size the same size or larger than your cutoffs?
Second, pulsing your system with 300K worth of energy all at once may
create some unpleasant results. Equilibration/slow heating might help.

Finally, what does the energy of the minimized system look like?
400 steps seems a wee bit short unless you have a small system.

Regards,
Brian

On Thu, 15 Apr 2004, Hua Wong wrote:

> I have a problem with setting up minimization.
> I start up with a protein with averagely good absolute deviation of omega torsion (used Procheck).
> And after using NAMD to minimize it, I end up with a minimized model but a rather awful lot of residues with abnormal deviation of omega torsion (Omega absolute mean deviation between 14 and 16)
>
> Am I doing something wrong or is it normal? Is there a setting I forgot?
>
> Here I join the .namd file I use to run NAMD.
>
> numsteps 10000
> timestep 1
>
> coordinates fooprot.pdb
> structure fooprot.psf
> parameters par_all22_prot.inp
> paraTypeCharmm on
>
> minimization on
>
> cutoff 20.0
> pairlistdist 20.5
> switching off
>
> exclude 1-4
>
> outputname fooprot_out
>
> IMDon on
> IMDfreq 1
> IMDport 3111
>
> temperature 300
> minimize 400
>
> run 200000
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
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