[gmx-users] Best force Field for Protein
Kovalskyy at uthscsa.edu
Tue Nov 20 03:03:00 CET 2018
>Then there are force fields that do better than others, but
>the choice must be yours based on a thorough review of available
Can you provide a list of FFs more suitable for folding and IDP simulations?
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Monday, November 19, 2018 5:46 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Best force Field for Protein
On 11/18/18 10:46 AM, Edjan Silva wrote:
> Dear Gromacs users, I will perform a simulation of a protein with explicit
> solvent to verify structural changes in temperatures of 300 k and 310 k.
I doubt any force field will give you any meaningful differences at such
a small temperature interval.
> Given the various force fields available on the gromacs platform, which one
> would be most appropriate for my experiment?
There's no real way to know. Different force fields do well at different
things. Simulating "a protein" can mean a lot of different things. Are
you simulating a well-folded protein with a stable tertiary structure?
If so, just about any modern force field will perform equivalently. Are
you trying to fold a protein or simulate something intrinsically
disordered? Then there are force fields that do better than others, but
the choice must be yours based on a thorough review of available
literature; it's not something that strangers on an Internet forum can
conclude for you :)
Justin A. Lemkul, Ph.D.
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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