[gmx-users] problem regarding total time elapsed

Dallas B. Warren Dallas.Warren at vcp.monash.edu.au
Thu Jul 26 02:56:15 CEST 2007

>After every run i am using the output gro file as an input for the next

Is that all you are using?  If that is the case, then not surprising it
is starting again.  What command line are you using?

You have not told it what the starting time is.  There is an option in
the mdp file if you use that (which in most cases your should).

What you should be doing is using tpbconv, feeding it the end .gro, .trr
and .edr files to it.  That command will take the frame times from the
.trr file, then use that to start the next set of simulations.

Also, ensure that you are actually saving the .trr with velocities and
locations at the end of the initial simulation (and probably a number of
times during as well so you don't loose things if it crashes).  As the
simulation set up by tpbconv will start off at the last spot in the .trr
file it can use.  If you only saved them at the start of the simulation,
then that is where it will start from.

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9524
When the only tool you own is a hammer, every problem begins to resemble
a nail.

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