[gmx-users] Continue simulation
js at drugdiscoveryathome.com
Wed Nov 25 01:44:58 CET 2009
I got it now. Thanks. Happy TG!
tpbconv -s md.tpr -extend 1 -o next.tpr
mdrun -s next.tpr -cpi md.cpt
Checkpoint file is from part 1, new output files will be suffixed part0002.
Reading file next.tpr, VERSION 4.0.5 (single precision)
Reading checkpoint file md.cpt generated: Tue Nov 24 15:00:12 2009
Gromacs binary or parallel settings not identical to previous run.
Continuation is exact, but is not guaranteed to be binary identical,
see the log file for details.
starting mdrun 'Protein in water'
1000 steps, 2.0 ps (continuing from step 500, 1.0 ps).
On Tue, Nov 24, 2009 at 7:20 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Jack Shultz wrote:
>> Is it ok just to use tpbconv, even though we get this message
>> "Continuation should be done by loading a checkpoint file with mdrun
> Please see the last paragraph in the "Version 4" section here:
>> I have tried mdrun using the -cpi flag
>> mdrun -v -x -c -o -e -cpo next.cpt -cpi md.cpt -deffnm md
>> Then when I run the next using the next.cpt, it seems to do the next
>> time interval because it is actually taking time to compute timesteps
>> mdrun -v -x -c -o -e -cpo next2.cpt -cpi next.cpt -deffnm md
>> using the checkpoint, i get less standard output telling me the
>> tototal simulation time
>> while preping the mdrun using tpbconv -s md.tpr -f md.trr -e md.edr
>> -time 2 -o next.tpr
> This is the obsolete way to continue a simulation, i.e. version 3.3.3 and
> earlier. Follow the instructions in the above link for version 4.
>> I get this output.
>> starting mdrun 'Protein in water'
>> 1500 steps, 3.0 ps (continuing from step 500, 1.0 ps).
>> step 500, will finish Wed Nov 25 00:15:43 2009
>> step 700, remaining runtime: 258 s
>> So should there be any difference in the results then?
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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