[gmx-users] Pressure swings during preliminary runs

[Justin A. Lemkul]

Warren Gallin wrote:
> HI,
> 
>     I am trying to simulate the behavior of short peptides in an aqueous 
> solution.
> 
>     When I look at the log of the progress of initial minimization runs 
> and longer production runs I am seeing crazy variations in the pressure, 
> including negative values and positive values well into the 100's of bar.
> 
>     The temperature is equilibrating and stable, so I am thinking that I 
> have missed some salient feature of the barostat.
> 
>     In one case I am not setting any of the relevant barostat 
> parameters, relying on the default values to work - is there someplace 
> where i can find waht the defaults values would be?
> 

Defaults are applied by grompp; the mdout.mdp file will show all default values 
if you haven't specified them.  Otherwise, check out:

manual.gromacs.org

The behavior you are seeing is quite normal.  See here:

http://oldwiki.gromacs.org/index.php/pressure

-Justin

>     In another case I am using the following settings in the .mdp file:
> 
> integrator      = md
> nsteps          = 50000
> dt              = 0.002
> nstlist         = 10
> rlist           = 1.0
> coulombtype     = pme
> rcoulomb        = 1.0
> vdw-type        = cut-off
> rvdw            = 1.0
> tcoupl          = v-rescale
> tc-grps         = protein non-protein
> tau-t           = 0.1 0.1
> ref-t           = 298 298
> Pcoupl          = Berendsen
> tau-p           = 1.0
> compressibility = 1e-5 1e-5 1e-5 0 0 0
> ref-p           = 1.0
> nstenergy       = 100
> define          = -DPOSRES
> 
> 
>     Can someone point me at some relevant information on how to 
> troubleshoot large rapid pressure variations?
> 
> Thanks
> 
> Warren Gallin
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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