Sindrila,
There are actually two options for such a restraint in AMBER, the nmropt
and ncsu_pimd module. Due to it being more actively supported, I would
personally recommend nmropt. Through experience I can anecdotally verify
that although the implementations are quite a bit different the results are
statistically identical.
The kind of restraint you want is available in nmropt in AMBER10 and later
(sander only) and is well documented in the latest AMBER manual (although,
in my opinion, somewhat covertly in the section "NMR, X-ray, and cryo-EM/ET
refinement", checkout section 6.1.1 on p. 201).
Regards,
Brian
On Fri, Feb 8, 2013 at 6:20 AM, Sindrila Dutta banik <
sindrila.duttabanik.yahoo.com> wrote:
> Dear all,
>
> I want to do umbrella sampling for a proton transfer process. I want to
> consider the reaction coordinate as a combination of two variables
> (difference between breaking bond and forming bond). I want a gradual
> change in this variable, like
>
> breaking bond length forming bond length RC
> 13.5-2.5
> 1.53.0-1
> 2.02.5 -0.5
> 2.52.00.5
> 31.51.5
> 3.512.5
>
> But I could not understand what would be the corresponding input file for
> the same in "type" section under &wt namelist. Is the type would be 'LCOD'
> or two distance under two name list section? How to write corresponding
> DISANG file?
>
> with best regards
> sindrila
> _______________________________________________
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> 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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Received on Fri Feb 08 2013 - 06:30:04 PST
