GROMACS modification: Yes/No
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What is the exact way to elongate a simulation after finishing 1st run?
I have run a simulation for 5ns and then used the .cpt file to run for the next 5ns.
The md.mdp file contains,
continuation = yes
gen_vel = no
The gmx commands I have used are as follows,
gmx grompp -f md.mdp -c *NPT.gro -r *NPT.gro -n *.ndx -p *.top -t *NPT.cpt -o *MD1.tpr
gmx grompp -f md.mdp -c *MD1.gro -r *MD1.gro -n *.ndx -p *.top -t *MD1.cpt -o *MD2.tpr
When I was catenating two .xtc files, I found the start time of the second run was at 0. It was solved by using -settime and got a 10 ns trajectory.
I am curious if the velocities are read correctly from NPT to MD1 and then MD1 to MD2.
And what is the correct way to start the second trajectory (MD2) that should not start from t0 = 0.0 ps.
Waiting for your comments and suggestions.
Thank you in advance.