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.abra...@anu.edu.au
<mailto:mark.abra...@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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--
========================================
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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