From: Irene Newhouse (einew_at_hotmail.com)
Date: Thu Apr 10 2008 - 21:17:08 CDT

Thank you!
 
Irene> Date: Thu, 10 Apr 2008 17:05:18 -0500> From: petefred_at_ks.uiuc.edu> To: einew_at_hotmail.com> CC: vmd-l_at_ks.uiuc.edu> Subject: Re: vmd-l: Using namdenergy in batch mode to compute dihedral energies> > Hi Irene,> if you run namd with one pairInteraction group instead of two, you'll > end up getting internal energies (including dihedrals), which you should > then be able to parse to pull out the dihedral energy. Please note that > pairInteractions may behave in slightly unintuitive ways if you are > calculating bonded interactions for only a subset of a segment; for > example, if you have a set of bonded atoms 1-2-3 and you use atoms 1 and > 2 in the pair interaction group, you will end up getting energies for > both the 1-2 and 2-3 bonds. Similar logic extends to dihedrals. If you > want to have more fine grained control to measure a single dihedral > (rather than a dihedral energy for a chunk of your structure) you may > instead want to use vmd's measure energy command with bigdcd.> Best,> Peter> > Irene Newhouse wrote:> > Using the sample config file at > > http://www.ks.uiuc.edu/Research/namd/2.6/ug/node42.html I've been able > > to compute interaction energies> > for a trajectory in batch mode. I'd like to do the analogous thing for > > dihedral energies of certain parts of my structure, but I'm not sure > > how to modify the sample config file appropriately - what do I use in > > place of the pairIneraction lines? I don't want to call the namdenergy > > plugin through VMD because my trajectories are too long to load into > > VMD - not enough memory per node.> > > > Thanks!> > Irene Newhouse> >> > ------------------------------------------------------------------------> > Get in touch in an instant. Get Windows Live Messenger now. > > <http://www.windowslive.com/messenger/overview.html?ocid=TXT_TAGLM_WL_Refresh_getintouch_042008>
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