One option is to avoid checkpoint files all together. I personally use
a grompp/mdrun cycle of ~2h segments that was historically done in
order to utilize the -sort -shuffle options to gromacs 3. I found it
simpler to keep on doing the exact same thing in gromacs 4, even
though I no longer -sort or -shuffle. It appears to be working fine
for me. I suspect that you could do the same type of thing via tpbconv.
Chris.
-- original message --
Justin,
When using checkpoint files to continue a run, mdrun overrides the
output file names specified by putting ".partXXXX" before the file
extension.
I don't want it to do that, since I have already told it how I want
the output files to be named.
Is it possible to stop that happening?
Try using -append.
That adds it onto the previous files. Not what I want either.
Way I have been doing my simulations is in batches of 1ns. Things
drop out, stop, then get resubmitted to do another 1 ns. Before 4.0
have used tpb2conv -extend 1000 supplied with the energy and
trajectory files.
Minor thing I know, but when your various scripts are all set up to
use a particular format, life is easier if you keep things are they are.
Catch ya,
Dr Dallas Warren
Pharmacy and Pharmaceutical Sciences
Monash University
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