On 2/02/2011 3:38 AM, Sai Pooja wrote:
From the website:
"If you change the integrator or ensemble, you should pass the
checkpoint file to tpbconv only, not to mdrun, since the state might
change and thus output files can not be appended."
Where was that? It could use clarification.
Mark
So now instead of supplying the checkpoint file to mdrun I supply it
to tpbconv... does this assure that the simulations start from the
coordinates/velocities specified by the .cpt file?
Pooja
On Tue, Feb 1, 2011 at 11:20 AM, Sai Pooja <saipo...@gmail.com
<mailto:saipo...@gmail.com>> wrote:
Thanks Mark. So if the simulation doesn't start from the
checkpoint file, from where are the initial coordinates velocities
etc. taken from?... the trajectory files?
Also, I could not find the environment variable... and I am not
sure how to use one.
Pooja
On Tue, Feb 1, 2011 at 3:03 AM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> wrote:
On 1/02/2011 7:50 AM, Sai Pooja wrote:
I think I have figured out the reason. It is because I am
carrying out replica exchange (manual) after every mdrun. If
the exchange occurs, I exchange the checkpoint files, extend
the simulation by 500 steps and continue. The new simulation
starts from exchanged cptfile. It seems that whenever the
exchange occurs, the earlier log,traj files are not appended.
They are instead overwritten. the obv solution is to save and
index these files with the relevant replicas everytime an
exchange occurs.
This would have been good to know earlier. If replica-exchange
leads to the ensemble of the .tpr not matching the ensemble of
the .cpt, then IIRC 4.5.3 mdrun will refuse to start from the
.cpt, which means the subsequent mdrun will start from the
.tpr only. Certainly a non-appending mdrun prints a warning
(or error, I forget which) message to the log file, but
perhaps the use of -append (erroneously) doesn't do that.
Please have a look and see if that is the issue. There is an
environment variable that can be set to tell mdrun that you
(think you) know what you are doing mismatching .tpr and .cpt.
Mark
However, i have a more general question. Since mdrun still
runs with the exchanged checkpoint files and starts from the
point where the previous run ended, can I be assured that an
exchange has been affected - since tpr files correspond to
the "replica-box" and cpi to the most recent exchanged replicas?
Pooja
On Mon, Jan 31, 2011 at 2:33 PM, Sai Pooja
<saipo...@gmail.com <mailto:saipo...@gmail.com>> wrote:
I manually index checkpoint files after every mdrun. What
troubles me is the randomness with which -append fails/works.
For eg, I have a simulation which runs from 3ns, 1ps in 1
mdrun. Now oddly enough, the logfile starts from
1184ps(in the end, I do remember the one starting from 0
but that was overwritten it seems) and the rest is
appended uptil the 3000ps step. Why would append work
from 1184ps to 3000ps but not for the previous ones?Could
it have anything to do with the network/cluster? If that
is the case is it safer to create a new file everytime
and then concatenate them after say every 100ps?
Pooja
On Sat, Jan 29, 2011 at 6:52 PM, Mark Abraham
<mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 30/01/2011 10:39 AM, Sai Pooja wrote:
I would be happy to supply more information.. if
someone could please look into this.. otherwise I
will have to switch to storing every file and then
just concatenating them which seems like a rather
roundabout way of doing it.
As I suggested a few emails ago, are you sure that
-cpi file exists? If your numerical suffixes are
indexing restarts, then unless you've done some
manual copying that you haven't told us about, it
won't. Your filename scheme seems a bit contorted -
like you're trying to do the work that GROMACS 4.5.x
will just do for you if you let it.
Otherwise, you'll have to do some detective work with
gmxcheck on the -cpi to see what might be the issue.
In your case, an initial
mdrun -deffnm rex_3
(perhaps save some copies while you're experimenting)
and subsequently
tpbconv -extend <blah> -f rex_3 -o rex_3
mdrun -deffnm rex_3 -append
will work and be much simpler than whatever you're
trying to do with filenames :-)
Mark
On Fri, Jan 28, 2011 at 4:37 PM, Sai Pooja
<saipo...@gmail.com <mailto:saipo...@gmail.com>> wrote:
This is the command:
nbs submit -command
"(/usr/local/gromacs/4.5.1/bin/mdrun_mpi -s
rex_3.tpr -e rex_3 -c after_rex_3 -cpi restart3
-cpo restart3 -ap
pend -g rexlog3 -x rextraj3);" -nproc 1 -name
"GENHAM-DIHEDRAL-3" -mail start end
Pooja
On Fri, Jan 28, 2011 at 4:20 PM, Mark Abraham
<mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 29/01/2011 3:56 AM, Sai Pooja wrote:
Hi,
I am using tpbconv and mdrun to extend a
simulation. I use it with the append
option but the files still get
overwritten or erased. Can someone help
me in this regard?
Pooja
Commands (in python)
cmd = '(%s/tpbconv -extend %f -s
rex_%d.tpr -o rex_%d.tpr)'
%(GROMPATH,dtstep,i,i)
os.system(cmd)
time.sleep(1)
cmd = 'nbs submit -command "'
cmd += '(%s/mdrun_mpi -noh
-noversion -s rex_%d.tpr -e rex_%d -c
after_rex_%d -cpi restart%d -cpo
restart%d -append -g rexlog%d -x
rextraj%d >/dev/null); '
%(GROMPATH,i,i,i,i,i,i,i)
cmd += '" '
cmd += '-nproc 1 '
cmd += '-name "GENHAM-DIHEDRAL-%d"
'%(i)
cmd += '-mail start end '
cmd += '-elapsed_limit 16h >> rexid'
os.system(cmd)
More useful for diagnostic and
record-preservation purposes is to construct
the cmd string and print it to stdout (or
something).
At the moment it is far from clear that your
-cpi file exists for the new run.
Mark
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