Re: pump / force application

From: Arturas (in_ubique_at_yahoo.com)
Date: Thu Apr 11 2013 - 08:54:34 CDT

Thanks Jerome and Alex, I posted a message few days ago with very specific questions regarding TclForces and TclBC ('tcf forces and ccordinate wrapping'), but no response. I have tried both and stuck with issues: #1) TclForce: using TclForce I'm getting not wrapped coordinates; looks like coordinate just propagate from initial positions #2) TclBC: wrapping gives me absolutely different coordinates from the input - so I can not control the location of "pump". I tried all 4 'wrapmode <>' types under tclBC and coordinates were the same. Any hints ? Thanks Art ________________________________ From: Jrme Hnin <jerome.henin_at_ibpc.fr> To: Axel Kohlmeyer <akohlmey_at_gmail.com> Cc: Namd List <namd-l_at_ks.uiuc.edu>; Arturas <in_ubique_at_yahoo.com> Sent: Thursday, April 11, 2013 8:15 AM Subject: Re: namd-l: pump / force application And more specifically, this sounds like a job for either Tcl boundary forces or for grid forces, although I am not very familiar with the latter. Best, Jerome ----- Original Message ----- > On Thu, Apr 11, 2013 at 3:19 PM, Arturas <in_ubique_at_yahoo.com> wrote: > > > > Hi everyone, > > > > Any ideas or suggestions how to construct a pump in NAMD to apply > > force for > > specific atoms and within a range of specific coordinates (e.g. Z) > > ? > > > http://www.ks.uiuc.edu/Research/namd/2.9/ug/node40.html > > > > > Best > > Art > > > > -- > Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 > International Centre for Theoretical Physics, Trieste. Italy. > >

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