[gmx-users] changing the time frame for simmulation

neelam wafa neelam.wafa at gmail.com
Thu Apr 12 20:02:07 CEST 2018


okay got it.
with dt =2fs    2500000 nsteps are for 5 ns simmulation.

On Thu, 12 Apr 2018 10:35 pm Justin Lemkul, <jalemkul at vt.edu> wrote:

>
>
> On 4/12/18 1:33 PM, neelam wafa wrote:
> > 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).
>
> Depends on dt. Please consider what the units are. This is a trivial
> calculation and is actually explained exactly in the comment field of
> the file you posted previously (and in the tutorial from which you got
> the file).
>
> -Justin
>
> > 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
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
> >> --
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
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