Re: minimization scripts

From: Tim Isgro (timisgro_at_ks.uiuc.edu)
Date: Mon Feb 09 2004 - 16:53:33 CST

Hi Gerald,

Your script looks OK, but you may need to minimize your system for more
than 400 steps. The "gradient tolerance" value in your NAMD output file
can give you a decent idea as to how well-minimized your system is. It is
a measure of the local energy landscape slope. When the value gets down
to around 10 or 20 you can feel pretty good.

As always, check the final structure with VMD (<-shameless plug) to make
sure there are no messy contacts.

Tim

On Mon, 9 Feb 2004, Gerald Quon wrote:

> Hi,
>
> I'm a new user and am interested in using NAMD for minimization purposes.
> I've downloaded the CHARMM potentials, and tried the following
> minimization script, but it does not
> seem to minimize my structures very well (when minimizing test native
> PDB files, I get structures that are 5-6 angstroms off).
>
> I was wondering if anyone could provide me with a 'standard' minimization
> script that I could start off with, or give me suggestions on how to
> improve mine? Thanks!
>
> - Gerald Quon
> University of Waterloo
> Waterloo, Ontario, Canada
>
> ------------------------
>
> # NAMD configuration file for PROT
> # molecular system
> structure 0.psf
>
> # force field
> paratypecharmm on
> parameters par_all22_prot.inp
> exclude scaled1-4
> 1-4scaling 1.0
>
> # approximations
> switching on
> switchdist 8
> cutoff 12
> pairlistdist 13.5
> margin 0
> stepspercycle 20
>
> #integrator
> numsteps 10000
> timestep 1
>
> #output
> outputenergies 1
> outputtiming 100
> binaryoutput no
> imdon yes
> imdfreq 1
> imdport 3111
>
> # molecular system
> coordinates 0.pdb
>
> #output
> outputname 0_out
> #dcdfreq 1000
>
> # constraints/Fixed
> fixedAtoms on
> fixedAtomsFile 0.pdb
> fixedAtomsCol B
>
> #protocol
> temperature 400
> langevin no
>
> rescaleFreq 50
> rescaleTemp 400
>
> #script
>
> minimize 400
>
> run 20000
>
>

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