[gmx-users] density vs time

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 16 22:38:32 CET 2010

Justin A. Lemkul wrote:
> nishap.patel at utoronto.ca wrote:
>> Hello,
>>     I am simulating one methane molecule in 899 water molecues in the 
>> box size of 3 3 3 nm (27nm^3). I would like to determine density vs 
>> time. Is there a way I can do that? I am running my simulation at 
>> constant Volume i.e. no pressure coupling. I tried using g_density but 
>> it gives me density vs box(nm).
>> Any suggestions would be useful.
> g_energy stores density information, except in the case of an NVT 
> ensemble.  If your box is fixed, so too is the density.

Edit: g_energy prints density, provided it is contained within the .edr file. 
In your case, it will not be.



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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