[gmx-users] Possible to stop mdrun changing file names when using checkpoint files?

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Feb 17 06:15:08 CET 2009

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.


-- original message --


>> 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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