[gmx-users] changing the time frame for simmulation

neelam wafa neelam.wafa at gmail.com
Thu Apr 12 10:11:37 CEST 2018

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?
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.

Further how can I set the parameters for a 5ns simmulation?

Thanks in advance.


More information about the gromacs.org_gmx-users mailing list