[gmx-users] Regarding extending simulations

[Dilip H N]

and which are the commands tht i need to give there.. gmx trjconv or gmx
grommp ..??
Can anybody guide me through this kindly..



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On Sun, May 21, 2017 at 4:40 PM, Dilip H N <cy16f01.dilip at nitk.edu.in>
wrote:

> Hello,
> I have ran a energy minimization, followed by nvt, followed by md run. My
> md run mdp (ie., md.mdp) has dt = 0.002, nsteps = 30000000 ; [0.002 *
> 30000000 = 60000 ps (60 ns)]
> nstxout = 5000 ; save coordinates every 10.0 ps
> nstvout = 5000 ; save velocities every 10.0 ps
> nstenergy = 5000 ; save energies every 10.0 ps
> nstlog= 5000 ; update log file every 10.0 ps
> nstxout-compressed = 5000      ; save compressed coordinates every 10.0 ps
>                                 ; nstxout-compressed replaces nstxtcout
> This simulation i have ran for 60 ns.
>
> Now i need extend the simulation for another 20ns, but with the change in
> md.mdp file as:-
> dt = 0.001, and nsteps = xxxx
> nstxout= 1000 ; save coordinates every 1.0 ps
> nstvout= 1000 ; save velocities every 1.0 ps
> nstenergy = 1000 ; save energies every 1.0 ps
> nstlog = 1000 ; update log file every 1.0 ps
> nstxout-compressed =1000; save compressed coordinates every 1.0 ps
> ie., i want the  dt time step of 0.001 and the outputs
> (nstxout,nstvout,etc.,) which can save the coordinates for every 1.0ps, for
> the 20ns run.
> I want to run the simulation for extra another 20ns by changing the md.mdp
> for 0.001 dt and saving the coordinates for every 1.0 ps.
> And thn i will have a complete run of total 80ns [(60ns of the 1st mdrun
>  of dt=0.002*30000000) + (next 2nd mdrun of dt=0.001*xxxx)].
>
> So wht are the changes tht i need to do in the mdp file.. if i change dt
> to 0.001and wht should be the nsteps(xxxx) value..and changing the output
> steps tht i want to save, such tht i get a run for 20ns , and which will
> give me a total of 80ns..
>
>
> Thank you
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
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>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student