[gmx-users] g_density options

[Mark Abraham]

You get the density by running g_energy. If you've tried that and seen that the density wasn't there, that would be because your volume is constant in an NVT simulation. grompp probably reported the density when you made the .tpr, however.

Mark

----- Original Message -----
From: vferrario at units.it
Date: Tuesday, October 12, 2010 23:14
Subject: Re: [gmx-users] g_density options
To: jalemkul at vt.edu, Discussion list for GROMACS users <gmx-users at gromacs.org>

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