[gmx-users] Umbrella pulling Drug + Ion channel
jalemkul at vt.edu
Tue Mar 25 11:11:20 CET 2014
On 3/24/14, 9:42 PM, Andres Ortega Guerrero wrote:
> The structure was equilibrated by an 30 ns NPT, and the structure is well equilibrated,
Was anything restrained during NPT? Previous equilibration is not equivalent to
proving that the present run succeeds without pull settings. What I'm getting
at is eliminating one variable at a time to figure out which element is failing.
> in the .log file appear this
> Step Time Lambda
> 8000 16.00000 0.00000
> Energies (kJ/mol)
> Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14
> 1.27298e+05 4.43493e+03 4.19453e+04 1.08477e+03 1.08744e+05
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 3.09243e+05 2.71776e+04 -2.48513e+04 -2.88816e+06 1.36779e+04
> COM Pull En. Potential Kinetic En. Total Energy Temperature
> 9.63822e+00 -2.27939e+06 4.02100e+05 -1.87729e+06 3.09322e+02
> Pres. DC (bar) Pressure (bar) Constr. rmsd
> -2.26609e+02 -8.75620e+00 2.51898e-05
An isolated snapshot from 16 ps isn't very informative, but suggests that you
have instability very early. None of these quantities is out of the ordinary.
I suggest you consult
especially with regards to outputting more frequently to track down what's
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
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