[gmx-users] Regarding extending simulations

Dilip H N cy16f01.dilip at nitk.edu.in
Sun May 21 13:10:52 CEST 2017

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,

Ph.D Student

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