[AMBER] Question about the implementation of the Steered MD

From: abdennour braka <abdennour.braka.univ-orleans.fr>
Date: Fri, 10 Mar 2017 08:26:36 +0100

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/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 09 2017 - 23:30:03 PST
Custom Search