[gmx-users] min + capped peptide
baharmehrpuyan at yahoo.com
Mon Nov 19 16:54:39 CET 2012
thanks Justin for the reply
sorry , I asked my question in a wrong way,
I mean should I do geometry optimization for that capped peptide(protein)?(with mm force field and steepest descent algorithm)
From: Justin Lemkul <jalemkul at vt.edu>
To: Bahar Mehrpuyan <baharmehrpuyan at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, November 19, 2012 6:55 PM
Subject: Re: [gmx-users] min + capped peptide
On 11/19/12 5:30 AM, Bahar Mehrpuyan wrote:
> Hi gmx users
> I want to cap my peptide (adding ACE & NAC) with Avogadro package , my question is , should I minimize the capped peptide with forcefields(molecular mechanics) available in avogadro, then use it in the simulation? or just simulation procedures (minimization and equilibration) is sufficient for minimizing the peptide structure.
This question does not make sense to me. All sensible workflows involve minimization and equilibration steps, which are distinct. Minimization is a non-dynamical process that seeks a stable energy minimum to begin the simulation. Equilibration prepares the system for data collection by optimizing solvent around the solute (and maybe other factors, depending on what's in the system) and establishing a stable thermodynamic ensemble.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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