[gmx-users] Pressure swings during preliminary runs

Warren Gallin wgallin at ualberta.ca
Tue Aug 25 21:18:51 CEST 2009


	I am trying to simulate the behavior of short peptides in an aqueous  

	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?

	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?


Warren Gallin

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