[gmx-users] Managing long simulations GMX 2018

R roli.singh at aol.com
Thu Mar 15 21:13:41 CET 2018

 Dear all,

I plan to run a long simulation for my protein of interest. However, I want to write trajectory files in batches of 1ns simulation. Thus, my plan is to run simulation for 1ns (to get files like md_1.* e.g.) and then extend it further for another ns and output be written in md_2.* files. Having run 1ns simulation, I did following:

--> gmx convert-tpr -s md_1.tpr -extend 1000 -o md_2.tpr

--> gmx mdrun -s md_2.tpr -cpi md_1.cpt --noappend

However, this gave outputs:  state.cpt, state_prev.cpt, traj.part0002.trr, traj_comp.part0002.xtc, confout.part0002.gro, ener.part0002.edr.

My questions are following:

1) Am I following the right way to extend the simulation?

2) Is there a way to get output files with md_2.* names or I need to rename outputs to names I am interested in i.e. mv traj.part0002.trr md_2.trr etc?

3) Where can I read more about differences between state.cpt and state_prev.cpt?

I am back to simulations after years, last I used was gromacs 3.x series. Things are bit different now !

Thanks a lot for your help.

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