Thanks Brian.
I'll keep that in mind.
On Thu, Sep 27, 2012 at 9:49 AM, Brian Radak <radak004.umn.edu> wrote:
> Vivek,
>
> Minimization and equilibration in AMBER *can* be done with icfe and ifsc
> flags (and obviously without as well). Whether or not one *should* do those
> steps with/without TI flags is another matter.
>
> There has been some discussion in the literature about "Hamiltonian
> lagging" (although I can't name any specific articles at present). That is,
> the time needed to find large Boltzmann weight configurations after
> switching Hamiltonians is much longer than one might expect (*i.e.* too
> long) and therefore a long equilibration without TI flags is potentially
> inadequate. Whether or not this is true for your system is an open
> question.
>
> Regards,
> Brian
>
> On Thu, Sep 27, 2012 at 11:20 AM, Vivek Shankar Bharadwaj <
> vbharadw.mymail.mines.edu> wrote:
>
> > Hi there,
> >
> > I am attempting to perform TI calculations for my enzyme system.
> >
> > I was wondering if the the Minimizations and Equilibration steps can be
> > done independent of TI calculations i.e. Do the minimizations and
> > equilibration MD runs w/o the ifsc icfe flags in the input.
> >
> > --
> > Vivek S. Bharadwaj
> > Graduate Student
> > Department of Chemical and Biological Engg.
> > Colorado School of Mines
> > Golden Colorado
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > 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
> address.
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--
Vivek S. Bharadwaj
Graduate Student
Department of Chemical and Biological Engg.
Colorado School of Mines
Golden Colorado
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Received on Thu Sep 27 2012 - 09:30:03 PDT
