From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu May 27 2021 - 04:28:37 CDT
----- On 27 Mai 21, at 9:30, M. A <matabay2010_at_gmail.com> wrote:
> Dear All,
> I am running MD simulation of ligand and protein interaction with the FEP method
> for calculation of free energy parameter. As is mentioned in page 36 of the
> related tutorial (In silico alchemy: tutorial for alchemical free-energy
> perturbation calculations with NAMD), we can measure the free-energy cost
> incurred for fading out pseudo bonds by zeroing out reversibly the associated
> force constants, until the aforementioned contribution due to the loss of
> translational entropy be recovered. Does anybody know how we can decrease the
> value of K in the extrabond section of namd config file?
The force constant is part of the extrabonds file. You will need a different extrabonds file for each value of the force constant. You can generate them with the scripting language of your choice. Then you need to run a NAMD simulation using each of the extrabonds files.
> I need the exact script
How much are you willing to pay someone to do that for you?
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