Re: restart a job

From: Life Sciences Inc (
Date: Wed Apr 06 2016 - 12:40:28 CDT

You don't have to mention the last time step as first time step in NAMD
input file, if you do its a good practice for your self by making new input
files for every run but its not necessary. One thing in restarting the job
is mentioning the previous coordinates, velocities and extended system
files with the options

binCoordinates $inputname.coor ;# coordinates from last run (binary)
binVelocities $inputname.vel ;# velocities from last run (binary)
extendedSystem $inputname.xsc ;# cell dimensions from last run

And give the numsteps as 500000 (your job depends on the numsteps,
multiply by time step to get the total time in ps to further run your
simulation by run command in the input file), after that you can
concatenate your dcd files using CATDCD which you can easily install.
You can check number of frames and simulation time with the same tool
and can also concatenate the trajectory for the exact time you wish to
have for simulation.

On Wed, Apr 6, 2016 at 9:57 PM, Farideh Badalkhani Khamseh <> wrote:

> Dear NAMD users,
> I am a beginner in NAMD and have a question about restarting a job. If I
> want to restart a job is it necessary to change the first time step to the
> last time step of previous run? and Should I decrease the number of time
> steps of run?
> I mean if the job stops at 200000 and I want to run 500000 simulation
> should I change run to 300000?
> Best.,
> F

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