[gmx-users] energy minimization_note

[Justin Lemkul]

On 7/19/18 6:18 AM, Atila Petrosian wrote:
> Dear Mark,
>
> Thanks for your answer.
>
> “But typically EM in vacuum is short enough you should not consider
>
> optimizing it.”. You are right. Using the reference manual about PME,
>
> I created new mdp file as follows:
>
>
>
> integrator               = steep
>
> nsteps                   = 50000
>
> emtol                    = 10
>
> emstep                   = 0.01
>
> ns_type                  = grid
>
> rlist                    = 0.9
>
> coulombtype              = PME
>
> Cutoff-scheme            = Verlet
>
> vdwtype                  = Cut-off
>
> rcoulomb                 = 0.9
>
> rvdw                     = 0.9
>
> constraints              = none
>
> periodic_molecules       = yes
>
> fourierspacing           = 4
>
> ewald_rtol               = 1e-5
>
>
>
> This time I have not previous note in grompp command.

You shouldn't hack at cutoff values to try to improve performance. 
Cutoffs are part of the force field. As Mark said, performance in energy 
minimization is usually not of much importance, but even if you see this 
note in preparing your MD simulations, you shouldn't just play with 
settings to try to make things run faster.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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