From: Irene Newhouse (einew_at_hotmail.com)
Date: Sun Apr 13 2008 - 11:47:03 CDT

I've written a script, but I'm having trouble figuring out how to deploy it in command line, text mode, of all things. No matter
what I try, the system claims 'bigdcd' is an invalid command - even when I add the full path to bigdcd, explicitly. Thanks!
Irene

From: einew_at_hotmail.comTo: petefred_at_ks.uiuc.eduCC: vmd-l_at_ks.uiuc.eduSubject: RE: vmd-l: Using namdenergy in batch mode to compute dihedral energiesDate: Thu, 10 Apr 2008 16:17:08 -1000

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>

Use video conversation to talk face-to-face with Windows Live Messenger. Get started!
_________________________________________________________________
Going green? See the top 12 foods to eat organic.
http://green.msn.com/galleries/photos/photos.aspx?gid=164&ocid=T003MSN51N1653A