[gmx-users] Regarding extending simulations with change in .mdp file

[Mark Abraham]

Hi,

gmx grompp -f first -o first
gmx mdrun -deffnm first
gmx grompp -f second -o second
gmx mdrun -deffnm second -cpi first

does what I think you should want. You end up with output files named
first.* and second.* which you can concatenate with trjconv or eneconv if
what you plan to do with them will tolerate the change in per-frame spacing
(NB don't assume any tool actually is capable of agreeing with your
intuition here).

It is technically feasible to arrange mdrun to append to the old files from
the new tpr, but you end up with a data curation problem, because you lose
the metadata that these were different stages, even though all you did was
change output frequency.

Mark

On Mon, May 22, 2017 at 5:35 AM 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 = 20000000
> 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;
>                                        ;nstxout-compressed replaces
> nstxtcout
> 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 md run.
>
> And then i need to have a  complete run of total 80ns [(60ns of the 1st
> mdrun  of dt=0.002*30000000) + (20ns of the 2nd mdrun of
> dt=0.001*20000000)].
>
>
> How can i do this..??
>
> Thank you.
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
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