[gmx-users] Fwd: Help with Gromacs 5.1 mdp options for CHARMM27 force field

[Justin Lemkul]

On 12/12/15 9:08 PM, Rakesh Ramachandran wrote:
> Hi Justin,
>
>     Thanks for the reply. Why is the RMSD difference reported by gmx energy
> tool so large after NPT equilibration as well as energy minimization ? I
> did not find such difference in RMSD when I superimposed the structures
> onto the crystal structure.
>

RMSD in this context is the standard deviation.

> *Energy Min*
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Potential                -1.27808e+06      45000     120456    -293146
>   (kJ/mol)
>

The average potential during EM is nonsense.  The purpose of EM is to 
progressively reduce the forces (and thus potential).  Plot the curve; you will 
see that an average is useless here.

> *NPT equil*
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Pressure                  -0.905575        1.8    99.0051    9.72043  (bar)
>

Please do some Googling for this; it comes up practically every week on this list.

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

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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