Jack Shultz wrote:
Hello,
I would like to setup a screensaver to visualize structures as we are
simulating them. We want to avoid slowing down the simulation
significantly. I found a solution that read pdb files. Is there a way
to reduce the frequency mdrun updates the confout.gro?
The structure file (-c) contains the coordinates and velocities of the last step
-c confout.gro Output Structure file: gro g96 pdb
if I increase these values, does it write to these files less
frequently or are we stuck with the updating this structure every
step?
nstxout: (100) [steps]
frequency to write coordinates to output trajectory file, the last
coordinates are always written
nstvout: (100) [steps]
frequency to write velocities to output trajectory, the last
velocities are always written
The confout.gro file is the last output of mdrun; it is written once (hence
"coordinates and velocities of the last step") and thus is unaffected by nst*
options, which only affect the trajectory.
-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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