[gmx-users] Extending simulation not work: always re-start from the beginning

[Zhang, Cheng]

Dear Gromacs expert,

I was trying to extend my simulations. Relevant files can be found at

https://copy.com/c8dDMnC0df2gbig9


To prepare the "md_0_1.tpr" file, I set the following in the "md_50ns.mdp" so that it can run 50 ns in total.


nsteps = 25000000

dt    = 0.002


Then I submit the same job for 5 times with the following command:


gerun mdrun_mpi -deffnm md_0_1.tpr -cpi md_0_1.cpt -maxh 30 -append

(Each of the 5 jobs would be hold until the previous one had finished.)


However, as I check the 5 xtc files (e.g. RMSD):


#md_0_1.tpr.xtc.1#

#md_0_1.tpr.xtc.2#

#md_0_1.tpr.xtc.3#

#md_0_1.tpr.xtc.4#

md_0_1.tpr.xtc


all of them start the simulation from 0 to 10000 ps with different fluctuations. As I understand, they all start from the beginning instead of extending the simulation based on its previous one.


So can I ask if I have done something incorrect?


Thank you.


Yours sincerely

Cheng