[gmx-users] NVT run

[Justin A. Lemkul]

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 
step."...

> 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.

-Justin

> Regards, Thomas

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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