[gmx-users] Density

[Justin A. Lemkul]

Carla Jamous wrote:
> Thank you Mark, for your answer.
> This time I have another issue: temperature.
> What are the ways to control temperature in gromacs (during heating or 
> equilibration phases), other than temperature coupling?
> 

I don't see how that's even possible.  By definition, temperature control is the 
job of a thermostat.  The sd integrator provides this function as well, by way 
of a Langevin thermostat, but that's really the same thing as using temperature 
coupling, anyway, it's just not a "tcoupl" option.

-Justin

> Thank you
> Carla
> 
> On Thu, Jan 14, 2010 at 10:40 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
> 
>     Carla Jamous wrote:
> 
>         Hello,
>         I'm experiencing some difficulties with gromacs. In order to
>         control my system's density, I have to use g_energy or g_density.
> 
> 
>     Those tools report density-related quantities, they do not control it.
> 
> 
>         However, when I use g_energy, in my list, "Density" doesn't appear.
> 
> 
>     g_energy doesn't report the density if you have a constant-volume
>     simulation (but grompp probably reported it when you generated the .tpr)
> 
> 
>         Else, if I use g_density, it needs a file traj.xtc which I don't
>         have.
> 
> 
>     Per Erik's point, you can usually use any coordinate file or
>     trajectory file.
> 
>     Mark
> 
> 
>         So please can anyone tell me how to check my system's density in
>         gromacs?
> 
>         Thank you
> 
>         Carla
> 
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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

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