[gmx-users] changing the time frame for simmulation
jalemkul at vt.edu
Thu Apr 12 19:13:44 CEST 2018
On 4/12/18 4:11 AM, neelam wafa wrote:
> 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
> Output control
> 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.
You do not need to change the amount of equilibration.
> Further how can I set the parameters for a 5ns simmulation?
It's the same math that you did above.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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