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

[Dilip H N]

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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