[plumed-users] rerun s/z path with gromacs
Ben Cossins
I have run a s/z path well tempered metadynamics calculation and
after 25 ns the protein leaves the periodic box which caused the path
variable to get messed up. I dont have velocity information with
which to restart the run before it left the box having added the
ALIGN_ATOMS list to my plumed.dat file.
Is it possible for me to rerun my simulation with gromacs and the
ALIGN_ATOMS list included to recalculate my HILLS file. Will this
recalculated data be correct?
Thanks
Ben
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Giovanni Bussi
sorry for the long delay. I guess it is too late but I will answer anyway...
If I understood correctly, you did NOT use ALIGN_ATOMS in the first
simulation, and now you want to restart it with ALIGN_ATOMS.
If you now rerun (with -rerun) your trajectory and recalculate the CVs
with ALIGN_ATOMS you should be able to find the point where the atoms
where not aligned anymore (i.e. when the new COLVAR and the old COLVAR
have the first inconsistent line), and restart from there.
The fact that you don't have the velocities is not a major problem,
since re-initializing them (at the restart) you will not affect the
free energy landscape.
Otherwise, as you said, you just repeat the calculation with
ALIGN_ATOMS. If you need further help in the ALIGN_ATOMS option write
again on the list...
Giovanni