[gmx-users] Further discussion: the -extend function of the tpbconv command

[Mark Abraham]

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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