[gmx-users] changing the time frame for simmulation

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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