[gmx-users] Umbrella pulling Drug + Ion channel

[Justin Lemkul]

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 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System, 
especially with regards to outputting more frequently to track down what's 
failing first.

-Justin

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

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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