Hi, Abdennour
If you are using jar to do SMD, the spring constant here is k instead of
1/2k. So if you are setting
rk2=100, the spring constant is 200
Best
Feng
On Fri, Mar 10, 2017 at 2:26 AM, abdennour braka <
abdennour.braka.univ-orleans.fr> wrote:
> Hi All,
> I have a quation about the implementation of the Steered MD in PMEMD.
> I read in the manual that: the center of the restraint is time-dependent
> as in
> Vrest (t) = (1/2)k[x − x0 (t)]2
> and I read in the manual of WHAM that Amber does not include the 1/2
> when specify spring constants for the restraint terms (umbrella sampling
> only ... ???)
> Would it be possible to confirm to me that in amber it is 1/2 k for the
> jar (SMD) simulations.
> Many thanks
> --
> Abdennour BRAKA
> /PharmD, PhD Student
> Structural Bioinformatics & Chemoinformatics
> Institut de Chimie Organique et Analytique (ICOA)
> UMR CNRS-Université d'Orléans 7311
> Université d'Orléans
> Rue de Chartres
> F-45067 Orléans
> phone: +33 238 494 577/
> _______________________________________________
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>
--
Feng Pan
Ph.D. Candidate
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Fri Mar 10 2017 - 09:00:04 PST
