[gmx-users] g_density options

vferrario at units.it vferrario at units.it
Tue Oct 12 14:13:14 CEST 2010

Thanks a lot, but... How can I exctract density information by using g_energy?


"Justin A. Lemkul" <jalemkul at vt.edu> ha scritto:

> 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:
> http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive
> -Justin
> -- 
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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