I have run the simulation using Gromacs forcefield for 1000 ps. Now I want to extend it to 10000 ps. How should I proceed? According to gromacs documentation, it can be done by changing the time in .tpr file, but we can't open it.
1) use "tpbconv" to extend simulation time in tpr file. You may use either "-extend" or "-nsteps" to extend simulation time.
2) use new tpr with mdrun and also use "-cpi" to input checkpoint file from last simulation.
thanks for your suggestions. According to documentation, we should use the following commands-
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt
Please tell me Is the previous tpr means the full.tpr generated after running the 1000 ps simulation? what is the timetoextendby- Is it like 9000 (extend by time) if we want to extend it to 10000 ps or is it 10000 ps and do we have to write ps also in it? What is the next.tpr, Is it the new tpr generated after extending the time? what is previous.cpt? Is it the state.cpt or prev_state.cpt? Which cpt file should we use?
Your suggestions would be highly appreciable.
Your steps are correct.
Previous.tpr is same tpr which you used for 1000 ps simulation.
Previous.cpt is state.cpt obtained in last 1000 ps simulation.
Default time unit is ps, so "-extend 9000" is correct for extension upto 10000 ps.
What I have to do after the creation of new.tpr?
How can I "append" the new.tpr with old.tpr and how can i evaluate rmsd or .gro?
Archit Garg You can extend the duration of simulation by looking into your md.mdp file. Here, the number of steps should be modified. For a duration of 200ns, I change it to 5000000*2= 10000000.
No need to change other values in case you only want to extend the time of simulation.
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