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On 2/02/2011 3:38 AM, Sai Pooja wrote:
<blockquote
cite="mid:AANLkTi=212vz4AzirsWh8Cyqc6KndFnbRUVKuFKpivD_@mail.gmail.com"
type="cite">
<div>From the website:</div>
<div> </div>
<div>"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."</div>
</blockquote>
<br>
Where was that? It could use clarification.<br>
<br>
Mark <br>
<br>
<blockquote
cite="mid:AANLkTi=212vz4AzirsWh8Cyqc6KndFnbRUVKuFKpivD_@mail.gmail.com"
type="cite">
<div>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?</div>
<div> </div>
<div>Pooja<br>
<br>
</div>
<div class="gmail_quote">On Tue, Feb 1, 2011 at 11:20 AM, Sai
Pooja <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:saipooja@gmail.com">saipooja@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="padding-left: 1ex;
margin: 0px 0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204);">
<div>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? </div>
<div> </div>
<div>Also, I could not find the environment variable... and I
am not sure how to use one.</div>
<div> </div>
<font color="#888888">
<div>Pooja<br>
</div>
</font>
<div class="gmail_quote">
<div>
<div class="h5">On Tue, Feb 1, 2011 at 3:03 AM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
</div>
</div>
<blockquote class="gmail_quote" style="padding-left: 1ex;
margin: 0px 0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204);">
<div>
<div class="h5">
<div bgcolor="#ffffff" text="#000000">
<div>On 1/02/2011 7:50 AM, Sai Pooja wrote:
<blockquote type="cite">
<div>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. </div>
</blockquote>
<br>
</div>
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.<br>
<font color="#888888"><br>
Mark</font>
<div>
<div><br>
<br>
<blockquote type="cite">
<div>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?</div>
<div> </div>
<div>Pooja<br>
<br>
</div>
<div class="gmail_quote">On Mon, Jan 31, 2011
at 2:33 PM, Sai Pooja <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:saipooja@gmail.com"
target="_blank">saipooja@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="padding-left: 1ex; margin: 0px 0px
0px 0.8ex; border-left: 1px solid rgb(204,
204, 204);">
<div><br>
I manually index checkpoint files after
every mdrun. What troubles me is the
randomness with which -append
fails/works.</div>
<div> </div>
<div>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?</div>
<div> </div>
<font color="#888888">
<div>Pooja<br>
</div>
</font>
<div class="gmail_quote">
<div>
<div>On Sat, Jan 29, 2011 at 6:52 PM,
Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
</div>
</div>
<blockquote class="gmail_quote"
style="padding-left: 1ex; margin: 0px
0px 0px 0.8ex; border-left: 1px solid
rgb(204, 204, 204);">
<div>
<div>
<div bgcolor="#ffffff"
text="#000000">
<div>On 30/01/2011 10:39 AM, Sai
Pooja wrote:
<blockquote type="cite">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.<br>
</blockquote>
<br>
</div>
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.<br>
<br>
Otherwise, you'll have to do
some detective work with
gmxcheck on the -cpi to see what
might be the issue.<br>
<br>
In your case, an initial<br>
<br>
mdrun -deffnm rex_3<br>
<br>
(perhaps save some copies while
you're experimenting) and
subsequently<br>
<br>
tpbconv -extend <blah> -f
rex_3 -o rex_3<br>
mdrun -deffnm rex_3 -append<br>
<br>
will work and be much simpler
than whatever you're trying to
do with filenames :-)<br>
<font color="#888888"><br>
Mark</font>
<div>
<div><br>
<br>
<blockquote type="cite"><br>
<div class="gmail_quote">On
Fri, Jan 28, 2011 at
4:37 PM, Sai Pooja <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="padding-left:
1ex; margin: 0px 0px
0px 0.8ex;
border-left: 1px solid
rgb(204, 204, 204);">
<div>This is the
command:</div>
<div> </div>
<div>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<br>
pend -g rexlog3 -x
rextraj3);" -nproc 1
-name
"GENHAM-DIHEDRAL-3"
-mail start end</div>
<div> </div>
<font color="#888888">
<div>Pooja<br>
<br>
</div>
</font>
<div>
<div>
<div
class="gmail_quote">On
Fri, Jan 28,
2011 at 4:20 PM,
Mark Abraham <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="padding-left:
1ex; margin:
0px 0px 0px
0.8ex;
border-left:
1px solid
rgb(204, 204,
204);">
<div>
<div>On
29/01/2011
3:56 AM, Sai
Pooja wrote:<br>
<blockquote
class="gmail_quote"
style="padding-left:
1ex; margin:
0px 0px 0px
0.8ex;
border-left:
1px solid
rgb(204, 204,
204);">Hi,<br>
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?<br>
Pooja<br>
Commands (in
python)<br>
cmd =
'(%s/tpbconv
-extend %f -s
rex_%d.tpr -o
rex_%d.tpr)'
%(GROMPATH,dtstep,i,i)<br>
os.system(cmd)<br>
time.sleep(1)<br>
cmd =
'nbs submit
-command "'<br>
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)<br>
cmd += '"
'<br>
cmd +=
'-nproc 1 '<br>
cmd +=
'-name
"GENHAM-DIHEDRAL-%d"
'%(i)<br>
cmd +=
'-mail start
end '<br>
cmd +=
'-elapsed_limit
16h >>
rexid'<br>
os.system(cmd)<br>
</blockquote>
<br>
</div>
</div>
More useful
for diagnostic
and
record-preservation
purposes is to
construct the
cmd string and
print it to
stdout (or
something).<br>
<br>
At the moment
it is far from
clear that
your -cpi file
exists for the
new run.<br>
<br>
Mark<br>
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