[gmx-users] NVT run

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 11 14:06:30 CET 2011

Thomas Koller wrote:
> Hello,
> I calculate the density of my lquid in the equilibrated time range of the
> density-time plots (NPT runs). I use the gro file of these NPT runs for NVT
> runs to calculate the self diffusion coefficient at the simulated density.
> Concerning this gro file: Is this taken from the end of the NPT run or the
> average of the equilibrated time range? Because this is important for the

mdrun -h:

..."The structure file (-c) contains the coordinates and velocities of the last 

> following NVT simulation. Which system size is listed there at the bottom of
> the output gro file?

The one corresponding to that configuration, i.e. the last step.


> Regards, Thomas


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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