On 5/04/2012 1:58 PM, Acoot Brett wrote:
Dear All,
According to
"http://www.gromacs.org/Documentation/How-tos/Extending_Simulations"; ,
the commands for extending MD are:
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt
But if you read
"http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File";,
it suggest for extension of MD, state.cpt should be used. But if we
use state.cpt for extension, in
"
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt
"
the "previous" in previous.tpr in tpbconv will be conflicting with
"previous" in previous.cpt in mdrun.
No, they are different files, of different file types, containing
different information and used in different contexts. If you were to
swap those filenames between the two commands, neither would work.
In addition in command
"
trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur
compact
"
can we change md_0_1.xtc to traj.xtc?
I am looking forward to getting a clarification from you.
The filename matters not. Whether it contains sensible raw material for
the trjconv operation given your objective matters.
Mark
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