[gmx-users] input error?

[Justin Lemkul]

On 7/31/14, 8:41 AM, Urszula Uciechowska wrote:
> I have changed the Pcoupl into parrinello-rahman and I have still the same
> error. The input file was taken from the martini webpage
> http://md.chem.rug.nl/cgmartini/index.php/proteins
>

 From my experience, the settings in the "equilibration.mdp" file are generally 
not very stable.  Without velocity generation, you get wild fluctuations in the 
thermostat.  Using Parrinello-Rahman for initial equilibration is an especially 
bad idea, because it leads to potentially large fluctuations in the box.

Fixes:

1. Generate velocities at the desired temperature with gen_vel and gen_temp.
2. Either use the Berendsen barostat (which is much more robust for initial 
equilibration) or do NVT for some time before even attempting NPT.

-Justin

>
> define           =  -DPOSRES
> dt               =  0.02
> nsteps           =  25000
> nstxout          =  0
> nstvout          =  0
> nstlog           =  100
> nstxtcout        =  100
> xtc-precision    =  10
> rlist            =  1.4
> coulombtype      =  shift
> rcoulomb         =  1.2
> epsilon_r        =  15
> vdw-type         =  shift
> rvdw-switch      =  0.9
> rvdw             =  1.2
> tcoupl           =  v-rescale
> tc-grps          =  Protein W
> tau-t            =  1.0 1.0
> ref-t            =  300 300
> Pcoupl           =  parrinello-rahman
> Pcoupltype       =  isotropic
> tau-p            =  12.0
> compressibility  =  3e-4
> ref-p            =  1.0
> refcoord_scaling =  all
>
> Urszula Uciechowska
> ~
>
>
> -----------------------------------------
> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
> http://www.ug.edu.pl/
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================