[gmx-users] Energy Minimization of Alanin

[Justin Lemkul]

On 9/19/12 6:04 AM, Lara Bunte wrote:
> Hello
>
> I want to do md simulations with the amino acid alanin for practice. I choose alanin because it is parametrized in my forcefield. I use charmm27.
>
> I created with pdb2gmx my topology and I use water model tip3p. I choosed a dodecahedron box with distance of 0.5 between the solute and this box. With genbox and the solvation I used spc216 model.
>
> Next I want to run an energy minimization and I create this em.mdp file:
>
> integrator         = steep
> emtol              = 1000.0
> emstep           = 0.01
> nsteps            = 5000
>
> nstlist             = 1
> rlist                = 0.7
> coulombtype   = PME
> rcoulomb        = 0.7
> vdw-type        = cut-off
> rvdw              = 0.7
> nstenergy      = 10
>
> grompp works but I got this note:
>
>
> NOTE 1 [file em.mdp]:
>    The optimal PME mesh load for parallel simulations is below 0.5
>    and for highly parallel simulations between 0.25 and 0.33,
>    for higher performance, increase the cut-off and the PME grid spacing
>
> Is this necessary for me to increase cut-off and PME grid spacing or can I ignore this note? I would be thankful if you could explain that to me.
>
>

For EM, the balance of PME vs PP interactions does not matter so much, so you 
don't necessarily need to take action for this reason.  If you are using 
CHARMM27, however, your cutoffs are completely wrong so you should correct them 
to have a sensible trajectory.

-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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