[gmx-users] Pressure scaling more than 1% please help new user

[Justin Lemkul]

On 6/23/14, 6:54 AM, Urszula Uciechowska wrote:
> Dear GROMACS users,
>
> I am working with gromacs and i have got a warning as
> shown below.Can you please suggest me what to do, to run my file
> completely.Please reply as soon as possible.Awaiting your suggestions.
> Step 8399 Warning: Pressure scaling more than 1%.
> DD step 8399 vol min/aver 0.653 load imb.: force 1.2% pme mesh/force 0.756
>
> Step Time Lambda
> 8400 16.80000 0.00000
>
>
> Step 8400 Warning: Pressure scaling more than 1%.
> Energies (kJ/mol)
> Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
> 2.54157e+05 1.41582e+04 1.06152e+05 1.08902e+05 4.41780e+05
> LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest.
> 4.77747e+05 -2.47518e+05 -2.41742e+07 -6.58090e+06 8.86258e+06
> Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
> -2.07371e+07 9.08915e+05 -1.98282e+07 5.84109e+01 -4.79084e+02
> Pressure (bar) Constr. rmsd
> 1.68607e+05 2.47297e-04
>
>
> Does this mean that I did not run the energy minimization long enough and
> there are some high forces? Is there something else that I am doing wrong?
>

Impossible to say without a complete description of (1) all your previous steps, 
(2) your actual .mdp file, and (3) what the system is.  Otherwise, all we can 
say is that your system is blowing up.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

> In my mdp file, the pressure coupling looks like:
> ; 7.3.15 Pressure Coupling
> pcoupl = parrinello-rahman ; pressure coupling where box vectors are variable
> pcoupltype = isotropic ; pressure coupling in x-y-z directions
> tau_p = 2.0 ; [ps] time constant for coupling
> compressibility = 4.5e-5 ; [bar^-1] compressibility
> ref_p = 1.0 ; [bar] reference pressure for coupling
>
> Thanks
> Urszula
>
>
> -----------------------------------------
> 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

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