[gmx-users] g_density options

[Justin A. Lemkul]

vferrario at units.it wrote:
> Thanks a lot, but... How can I exctract density information by using 
> g_energy?
> 

Have you tried it?  You're given a list from which to choose.  Type the number 
of the property you want (i.e., Density), then either a blank line or the number 
zero to terminate interactive selection.  This is documented somewhere in the 
manual.

-Justin

> 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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-- 
========================================

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

========================================