[gmx-users] question about continuation using tpbconv and mdrun -cpi

[Berk Hess]

Hi,

Your command line is incorrect.
-reprod should be used without yes.
-reprod is yes
-noreprod is no

mdrun -cpi has no effect on your results at all.
But always remember that MD is chaotic, there is no point in trying
to reproduce trajectories exactly, unless for a very special purpose.

Berk

> Date: Thu, 30 Jul 2009 16:53:13 +0200
> From: qiaobf at gmail.com
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] question about continuation using tpbconv and mdrun	-cpi
> 
> Hi Mark,
> 
> Sorry to trouble you again!
> 
> I made two tests, by using one-processor and one 32-processors on the
> same cluster. I used 4000SPC/E waters (OPLS-AA ff.) The former
> (one-processor) gives the exactly the same potential. However, the
> latter still shown some deviation of the potential. When I use "-reprod
> yes", the potential is -190098+-457.199 for "Comparison", and
> -190088+-467.225 for "Reference". When I use "-dlb no", -190116+-476.512
> for "Comparison", and -190114+-483.749 for "Reference".
> 
> The following is the job script lines when using "-reprod yes":
> ********************************************************************************
> # Reference
> grompp -f full.mdp -c initial.gro -p system.top -o full
> mpirun -np 32 mdrun -deffnm full -reprod yes
> 
> # Comparison
> grompp -f full.mdp -c initial.gro -p system.top -o full2
> mpirun -np 32 mdrun -deffnm full2 -reprod yes -cpt 2 -maxh 0.2
> mpirun -np 32 mdrun -deffnm full2 -reprod yes -cpi full2.cpt -append
> ********************************************************************************
> 
> Do you have some further ideas?
> 
> best wishes,
> Baofu Qiao
> 
> 
> Mark Abraham wrote:
> > Baofu Qiao wrote:
> >> Hi Mark,
> >>
> >> Thanks!
> >> Because the maximum time for one single job is set to be 24hours on the
> >> cluster I'm using, I want to make sure which is the best way to continue
> >> the gmx jobs. I wonder how strong effect "mdrun -cpi" has?  From the
> >> introduction of mdrun, it seems that there are some EXTRA energy frames,
> >> but for the trajectory file (.xtc), there is no extra frames? Am I
> >> right?
> >>
> >> "mdrun -h
> >> --> The contents will be binary identical (unless you use dynamic load
> >> balancing), but for technical reasons there might be some extra energy
> >> frames when using checkpointing (necessary for restarts without
> >> appending)."
> >
> > The intent with GROMACS 4.x is for a user to be able to construct a
> > .tpr with a very long simulation time, and perhaps constrain mdrun
> > with -maxh (or rely on the cluster killing the job), and to use the
> > information in the checkpoint file to restart correctly and perhaps to
> > then use mdrun -append so that when the simulation is running
> > smoothly, only one set of files needs to exist. Thus one doesn't need
> > to trouble with using tpbconv correctly, crashes can restart
> > transparently, etc. The old-style approach still works, however.
> >
> > Obviously you should (be able to) verify with mdrun -reprod that
> > whatever approach you use when you construct your job scripts leads to
> > simulations that are in principle reproducible. For production, don't
> > use -reprod because you will want the better speed from dynamic load
> > balancing, etc.
> >
> > Mark
> > _______________________________________________
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> >
> 
> 
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