Hi Giulia,
Thank you for the answer!
I think that it possible to do, have a look at this paper:
Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations. Wereszczynski J. & McCammon A. 2010. JCTC, 6, 3285-3292.
Cheers
Josephine
-----Original Message-----
From: giulia palermo [mailto:giulia.palermo83.gmail.com]
Sent: venerd́ 29 aprile 2016 20:47
To: AMBER Mailing List
Subject: Re: [AMBER] accelerated MD on set of dihedrals
Hi Giuseppina,
I don't think you really can.
aMD is unconstrained MD. This means that a boost potential is applied to all the dihedrals of your systems. This lets the system evolve without adding artificial reaction coordinates ..
however, check with the developers.
giulia
2016-04-29 9:56 GMT-07:00 Giuseppina La Sala <Giuseppina.LaSala.iit.it>:
> Hi everyone,
> I want to perform an accelerated MD simulation using only a specified set of dihedral angles of my protein.
> My question is: how do I edit the input file to specify the residues of interest?
> Thank you in advance
>
> Josephine
>
>
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Received on Fri Apr 29 2016 - 15:30:03 PDT
