[gmx-users] a question on rerun MD after computer crash

Emanuel Birru Emanuel.Birru at monash.edu
Wed Feb 6 06:01:05 CET 2013

Hi Acoot,

Better to use the following command

tpbconv -s md-0-1.tpr -extend (PUT HOW LONG YOU WANT TO RUN IN ps HERE) -o OUT_PUT.tpr
mdrun -s OUT_PUT.tpr -cpi md-0-1_prev.cpt 

You have to use your own proper naming and do not forget to put how long you should extend it in picosecond (for example if you want to extend for 4ns you should put 4000).


-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Acoot Brett
Sent: Wednesday, 6 February 2013 3:50 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] a question on rerun MD after computer crash

Dear All,

I have run a 5 ns MD by

mdrun -deffnn md-0-1

After about 1 ns the computer was out of power by accident. I tried to continue run the MD. From the on-line material there is a method "mdrun -s topol.tpr -cpi state.cpt".

But by the above mdrun -deffnn md-0-1, I find I got 2 cpt files, one is md-0-1.cpt, one is md-0-1-prev.cpt.

In order to continue my MD, will you please suggest I use

mdrun -s md-0-1.tpr -cpi md-0-1.cpt, or I use

mdrun -s md-0-1.tpr -cpi md-0-1-prev.cpt?

I am looking forward to getting your reply.


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