[gmx-users] Density

Justin A. Lemkul jalemkul at vt.edu
Fri Sep 9 15:16:24 CEST 2011

vferrario at units.it wrote:
> Dear all,
> I want to calculate the density of my system and visualize it during the 
> simulation time. I've tried with g_density and with g_energy but in all 
> the cases the density calculated is the average density all along the 
> simulation and not the density of all the system in each step of the 
> trajectory. How can I compute what I need?

g_energy should have printed an energy.xvg file that contains values printed 
every nstenergy steps.  It will not necessarily agree exactly with the average 
printed by g_energy, since the .edr file is accurate over all MD steps but the 
.xvg file contains data saved at only the requested output frequency.  So unless 
you set nstenergy = 1, you will not get density values over every step.


> Thanks a lot.
> Valerio
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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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