[gmx-users] changing the time frame for simmulation
neelam.wafa at gmail.com
Thu Apr 12 10:11:37 CEST 2018
Dear gmx users,
I have run the md simmulation of my protein ligand complex for 1ns
following the conditions used in tutorial by sir Justin. Now I want to run
the simmulations for 5ns and 10 ns. How have set it like this:
integrator = md ; leap-frog integrator
nsteps = 5000000 ; 2 * 5000000 = 10000 ps (10 ns)
dt = 0.002 ; 2 fs
Is it right?
Is it needed to change the output control as well. It is in this form
nstxout = 0 ; suppress .trr output
nstvout = 0 ; suppress .trr output
nstenergy = 5000 ; save energies every 10.0 ps
nstlog = 5000 ; update log file every 10.0 ps
nstxout-compressed = 5000 ; write .xtc trajectory every 10.0 ps
Please also guide me is it enough to run the last production md for 10 ns
with the npt and nvt run unchanged or I have change the time frame of the
equliberation steps as well.
Further how can I set the parameters for a 5ns simmulation?
Thanks in advance.
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