I think you are over equating the potential type (*i.e. *softcore) and the
analysis type (*i.e. *thermodynamic integration); they are essentially
independent.
Although the use of softcore potentials in AMBER assumes that you want to
do TI and therefore always collects the appropriate data, that doesn't mean
you have to use it for anything.
You should probably be aware that the softcore code in sander and pmemd are
implemented differently. Check the manual for details.
Brian
On Thu, May 8, 2014 at 12:44 PM, Asaminew Haile <ashaethio.gmail.com> wrote:
> Thanks Dac
>
> My interest is turn off VDW potential for selected regions in order to let
> atoms pass through each other.
>
>
>
>
>
> On Thu, May 8, 2014 at 12:32 PM, David A Case <case.biomaps.rutgers.edu
> >wrote:
>
> > On Thu, May 08, 2014, Asaminew Haile wrote:
> >
> > > I've an RNA molecule, with one single strand region and I would like do
> > > pulling by adding restraints. To do so, I need to turn on SOFTCORE
> > > potential. I'm aware of that in the amber manual, softcore potential is
> > > under the thermodynamic integration. I was wondering if someone has
> any
> > > idea how to use the softcore other than TI.
> >
> > Amber's "softcore" may not be what you think it is. Ours only works in
> the
> > context of TI. (If I'm forgetting something, others on the list can
> chime
> > in.)
> >
> > ...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Asaminew H. Aytenfisu, Grad Student
> David Mathews' group
> Department of Biochemistry and Biophysics
> University of Rochester Medical Center
> Office: 3-8807
> 601 Elmwood Avenue, Box 712
> Rochester, NY 14642
> (585) 275-1748
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
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Received on Thu May 08 2014 - 10:30:06 PDT
