vferra...@units.it wrote:
Dear all,
I want to calculate the density of my system and visualize it during the
simulation time. I've tried with g_density and with g_energy but in all
the cases the density calculated is the average density all along the
simulation and not the density of all the system in each step of the
trajectory. How can I compute what I need?
g_energy should have printed an energy.xvg file that contains values printed
every nstenergy steps. It will not necessarily agree exactly with the average
printed by g_energy, since the .edr file is accurate over all MD steps but the
.xvg file contains data saved at only the requested output frequency. So unless
you set nstenergy = 1, you will not get density values over every step.
-Justin
Thanks a lot.
Valerio
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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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