RE: Scripting: Handle for energy terms in the PSF file?

From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Wed Dec 12 2007 - 15:32:56 CST

Hi Peter,

   This is a good idea, but involves a bit more parsing than I'm
prepared to do for the task at hand. However, if the developers were to
add to "measure energy" the capability to take a parameter FILE as
input, as well as individual parameters, I think this might be a
generally interesting tool.

Thanks for the idea!

- Chris

> -----Original Message-----
> From: Peter Freddolino [mailto:petefred_at_ks.uiuc.edu]
> Sent: Tuesday, December 11, 2007 7:30 PM
> To: Chang, Christopher
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: Scripting: Handle for energy terms in the PSF
file?
>
> Hi Chris,
> did you try using measure energy dihed? I imagine the best way to do
> this would be to generate a dihedral list as you did for namdenergy
but
> instead use this command for the calculation. It should be *much*
faster
> because it doesn't have to invoke namd every time. You can find
> documentation for this at
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node124.html
> Note that you'll need to do a bit of parameter file parsing up front
to
> get the appropriate parameters for the dihedrals of interest.
>
> Best,
> Peter
>
> Chang, Christopher wrote:
> >
> > Hi,
> >
> >
> >
> > I am testing dihedral parameters, and am encountering nan's in
the
> > first energy minimization step associated with the dihedral energy
> > term. I would like to dump out the associated dihedral energy for
> > every term in the associated PSF file to track down the problem(s),
> > but I don't know what the handles are for this. So, along the
> > pseudocode lines of
> >
> >
> >
> > set temp [atomselect top "protein"]
> >
> > for PSF_dihedral_term in $temp:
> >
> > measure energy $PSF_dihedral_term;
> >
> >
> >
> > I've seen the NAMD PairInteraction option, but I'd still need a
handle
> > for the terms in the PSF file. mdenergy from Jan Saam is another
> > option, but I would have to merge two parameter files, which I'd
> > rather avoid.
> >
> >
> >
> > How do the pros do this?
> >
> >
> >
> > NAMD 2.6, 64-bit
> >
> > Opteron
> >
> > Linux
> >
> >
> >
> > Thanks,
> >
> >
> >
> > Chris
> >
> >
> >
> > Christopher H. Chang, Ph.D.
> > Scientist II
> > National Renewable Energy Laboratory
> > 1617 Cole Blvd., Mail Stop 1608
> > Golden, CO 80401
> > Phone (303) 275-3751
> > Fax (303) 275-4007
> >
> >
> >

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