[gmx-users] min + capped peptide

[Justin Lemkul]

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

-- 
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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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