[gmx-users] changing the time frame for simmulation
neelam.wafa at gmail.com
Thu Apr 12 19:33:50 CEST 2018
Thank you sir justin.
I am confused a bit. Kindly tell me which one of the following is right for
nsteps =5000000; 5000000=5000 ps (5ns)
nsteps = 2500000 ; 2*2500000= 5000 ps (5ns).
On Thu, 12 Apr 2018 10:13 pm Justin Lemkul, <jalemkul at vt.edu> wrote:
> 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
> > 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.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 303 Engel Hall
> 340 West Campus Dr.
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> jalemkul at vt.edu | (540) 231-3129
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