[gmx-users] Energy Minimization of Alanin

[Lara Bunte]

Hi

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. :-)

Greetings
Lara






----- Ursprüngliche Message -----
Von: Peter C. Lai <pcl at uab.edu>
An: Discussion list for GROMACS users <gmx-users at gromacs.org>
CC: 
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:
> 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. 
> 
> 
> Thanks for help
> 
> Greetings
> Lara
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==================================================================
Peter C. Lai            | University of Alabama-Birmingham
Programmer/Analyst        | KAUL 752A
Genetics, Div. of Research    | 705 South 20th Street
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