[gmx-users] changing the time frame for simmulation

[neelam wafa]

Thank you sir justin.
I am confused a bit. Kindly tell me which one of the following is right for
5 ns.
nsteps =5000000; 5000000=5000 ps (5ns)

or

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
> 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?
>
> Yes.
>
> > 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
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> Blacksburg, VA 24061
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>
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