Hi Berk,
Thanks for pointing out my mistake!
What I worry about is how big the deviation is after several
continuations? If it is unpredictable, it is a sad news.
regards,
Baofu Qiao
Berk Hess wrote:
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: qia...@gmail.com
To: gmx-users@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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