[gmx-users] g_density options

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 12 13:58:02 CEST 2010

Justin A. Lemkul wrote:
> vferrario at units.it wrote:
>> I'm a GROMACS user and I want to authomatize solvent parametrization in
>> GROMOS force-field. The parametrization of a solvent converg also on
>> the density. The problem is that g_density always ask on which element
>> of the system compute the density and it is waiting for a replay that
>> I can't authomatize. Is it possible to set the g-density calculation
>> on the whole system by default and skippink the choice step?
> If you're analyzing a homogeneous liquid system, then g_density is the 
> wrong tool.  It calculates density as a function of the box vector.  The 
> whole density of the system is written to the .edr file and can be 
> extracted using g_energy.

And if you're looking to automate any process in Gromacs, see the following:




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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