From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Dec 11 2007 - 20:30:22 CST
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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