AMBER Archive (2008)

Subject: AMBER: RE: About restart amber

From: Ross Walker (
Date: Fri Nov 21 2008 - 15:45:16 CST

Hi Zhou,


Such questions should really go to the AMBER mailing list which is where I
am copying this message. (See for signup details.


To answer your question, assuming the machine did not crash while writing
the restart file, you can restart the simulation in the same way that one
runs a single MD simulations in multiple steps. See for example how it is
done in section 6 of tutorial B1.


Essentially you create a new input file with irest=1 and ntx=5 and then run
sander or pmemd again providing the rst file from the crashed job as the
input coordinates (-c ...rst). The code will then continue running from the
point at which the last restart file was written - make sure you write to a
new output and mdcrd file so you don't overwrite the previous run.


If you still want the exact same length of calculation then you should look
in the top of the restart file where the simulation time that the restart
file corresponds to is written and then adjust nstlim in the new mdin file
accordingly. You might also need to manually clean up your output file so it
stops at the point at which the restart file was written (if ntpr /= ntwr).
The same is true for the mdcrd file although you will need to run this
through ptraj and have it write you a new mdcrd file containing all the
frames from 1 to the frame the restart file corresponds to.


Good luck,



From: z g []
Sent: Thursday, November 20, 2008 12:50 AM
To: Ross Walker
Subject: About restart amber


Dear sir :
        I have read the online Amber beginning tutorials, and learned a lot.
Thank you very much!
Here, I have some questions about using amber
I put a task on sander, during the simulation, some accident happened ( such
as power cut ), and my program stopped.
How can I restart the program and continue doing my simulations. Please tell
me the details about it
Thanks for your patience!

your sincerely
Zhou Gong


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