[gmx-users] min + capped peptide

[Justin Lemkul]

On 11/19/12 10:54 AM, Bahar Mehrpuyan wrote:
> 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)
>

You should do an energy minimization with whatever force field you intend to use 
for the simulations.

-Justin

>
> --------------------------------------------------------------------------------
> *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 <http://vt.edu/> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/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

========================================