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On 30/04/2012 6:34 PM, Steven Neumann wrote:
<blockquote
cite="mid:CAKZJqQF3opsSjJjgXByuj_iy0E5c0X_+-TXHyT8poDpWK4_9ag@mail.gmail.com"
type="cite"><br>
<br>
<div class="gmail_quote">On Fri, Apr 27, 2012 at 5:13 PM, Justin
A. Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px
0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div class="im"><br>
<br>
On 4/27/12 12:09 PM, Steven Neumann wrote:<br>
</div>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px
0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div class="im"><br>
<br>
On Fri, Apr 27, 2012 at 4:38 PM, Justin A. Lemkul <<a
moz-do-not-send="true" href="mailto:jalemkul@vt.edu"
target="_blank">jalemkul@vt.edu</a><br>
</div>
<div class="im"><mailto:<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>
wrote:<br>
<br>
<br>
<br>
On 4/27/12 11:34 AM, Steven Neumann wrote:<br>
<br>
<br>
<br>
On Fri, Apr 27, 2012 at 4:28 PM, Justin A. Lemkul
<<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br>
<mailto:<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
</div>
<div>
<div class="h5"> <mailto:<a
moz-do-not-send="true" href="mailto:jalemkul@vt.edu"
target="_blank">jalemkul@vt.edu</a> <mailto:<a
moz-do-not-send="true" href="mailto:jalemkul@vt.edu"
target="_blank">jalemkul@vt.edu</a>>>> wrote:<br>
<br>
<br>
<br>
On 4/27/12 11:22 AM, Steven Neumann wrote:<br>
<br>
Dear Gmx Users,<br>
<br>
I am running 2 us simulation in implicit
solvent model:<br>
<br>
define = -DPOSRES<br>
integrator = sd ; leap-frog
integrator<br>
nsteps = 500000000 ; 0.004 *
500000000= 2 us<br>
dt = 0.004 ; 4 fs<br>
; Output control<br>
nstxout = 0<br>
nstxtcout = 50000 ; xtc
compressed trajectory output<br>
every 2 ps<br>
nstenergy = 10000 ; save energies
every 2 ps<br>
nstlog = 10000 ; update log
file every 2 ps<br>
<br>
How come my trajectory (trr) is being
created and takes 80 GB?<br>
<br>
<br>
The default for nstvout is 100, so you're
likely getting very frequent<br>
output of velocities into the .trr file.<br>
<br>
-Justin<br>
<br>
Thank you<br>
This job crashed due to the quota exceeded. If
change my mdp file (with<br>
additional nstvout=0) using tpbconv and run it
from the checkpoint file it<br>
should work then with no trr file?<br>
<br>
<br>
If you need to change the .mdp file, you can't use
tpbconv; use grompp to<br>
generate a new .tpr file and submit the new job.<br>
<br>
<br>
So if I will create new mdp file (with additional
nstvout=0 to get rid of trr<br>
files) and use:<br>
<br>
mdrun -s new.tpr -cpi last.cpt<br>
<br>
Will I continue from the checkpoint?<br>
<br>
</div>
</div>
</blockquote>
<br>
That's the question I posed below...
<div class="im"><br>
<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px
0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote"> I'm
not sure if you can pick up using mdrun -cpi if the
settings have<br>
changed, but you can try.<br>
<br>
<br>
Yes you can, from 4.0 you do not have to specify -append
just -cpi file if the<br>
job crashed.<br>
<br>
</blockquote>
<br>
</div>
I am aware of checkpointing, but what I'm not sure of is if
you change output options (or others) mid-stream, if the
checkpointing mechanism will complain, particularly due to the
changes in the .trr content. You'll have to try and see.
<div class="HOEnZb">
<div class="h5"><br>
<br>
-Justin<br>
</div>
</div>
</blockquote>
<div> </div>
<div> </div>
<div>Indeed, it complains in terms of not present trr file (3
out of 4 files present) and he does not want to carry on. But
when I change name of the output it starts from the
checkpoint generating new files. </div>
</div>
</blockquote>
<br>
Yes, that will be the effect of the (default) mdrun -append yes in
4.5<br>
<br>
<blockquote
cite="mid:CAKZJqQF3opsSjJjgXByuj_iy0E5c0X_+-TXHyT8poDpWK4_9ag@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div>Can I then somehow connect those two xtc trajectories using
trjconv?</div>
</div>
</blockquote>
<br>
Yes, or better trjcat. Be sure to read and understand their -h
output first.<br>
<br>
<blockquote
cite="mid:CAKZJqQF3opsSjJjgXByuj_iy0E5c0X_+-TXHyT8poDpWK4_9ag@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div> Which tpr file I should use?</div>
</div>
</blockquote>
<br>
You don't even need a .tpr file to concatenate trajectory files.<br>
<br>
Mark<br>
<blockquote
cite="mid:CAKZJqQF3opsSjJjgXByuj_iy0E5c0X_+-TXHyT8poDpWK4_9ag@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div> </div>
<div>Steven</div>
<div> </div>
<div> </div>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px
0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div class="HOEnZb">
<div class="h5"><br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true"
href="http://vt.edu/" target="_blank">vt.edu</a> | <a
moz-do-not-send="true" href="tel:%28540%29%20231-9080"
target="_blank" value="+15402319080">(540) 231-9080</a><br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- <br>
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