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 <jalem...@vt.edu>
*To:* Bahar Mehrpuyan <baharmehrpu...@yahoo.com>; Discussion list for GROMACS
users <gmx-users@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
========================================
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