[gmx-users] pressure RMSD

[Justin Lemkul]

On 7/21/16 2:07 AM, roshanak starlight wrote:
> hello
>
> i did npt mdrun for kalp-15 in dppc and then I analyzed the pressure
> progression by using g_energy .i selected box-x and box-y and also pressure.
>
> the average of boxes were almost 6/4 and RMSD was 0/097
>
> but about pressure , average was 1/037 and RMSD was 203/282 !
>
> about pressure : Why the RMSD is so great ( but average is near to
> reference ) ?
>

This question gets asked weekly.  Use Google :)  It will surely point you to:

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

and other discussions on the magnitude of pressure fluctuations and how they 
depend on the system.

-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

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