[gmx-users] min + capped peptide

[Bahar Mehrpuyan]

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

-- ========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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