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
====================================================================
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Received on Thu Sep 27 2012 - 09:00:04 PDT
