[gmx-users] Energy Minimization of Alanin
lara.bunte at yahoo.de
Wed Sep 19 18:07:03 CEST 2012
Thanks for the help. I changed this cut-off parameters and increased the distance between my box und the solute from 0.5 to 1.5. I got no error and no note. :-)
----- Ursprüngliche Message -----
Von: Peter C. Lai <pcl at uab.edu>
An: Discussion list for GROMACS users <gmx-users at gromacs.org>
Gesendet: 12:12 Mittwoch, 19.September 2012
Betreff: Re: [gmx-users] Energy Minimization of Alanin
for EM you can probably ignore this, but note that these are the wrong
cutoffs for CHARMM27. (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 rvdw=1.2
rvdw_switch=0.8 and vdwtype=switch).
On 2012-09-19 11:04:47AM +0100, Lara Bunte wrote:
> 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.
> Thanks for help
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Peter C. Lai | University of Alabama-Birmingham
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