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On 15/07/2011 12:40 AM, Sheeba Jem wrote:
<blockquote
cite="mid:CABUNsPc_kVpARtg0xz+WB01urGtsc+WeyBcKTXPHC6AWWVyLcw@mail.gmail.com"
type="cite"><br>
Hi, I had been trying different thermostats, barostats, time steps
and coupling times to get remd for the peptide lipid system
working and I had even equilibrated each replica for 50 ns before
submitting them to remd. However none of them work when I use one
processor per replica. That is, I have 50 replicas and when I
submit the job with 50 processors the job crashes with the bad
contacts error.</blockquote>
<br>
How soon? Under what REMD regime? The volume scaling required for
NPT REMD can occasionally be problematic.<br>
<br>
<blockquote
cite="mid:CABUNsPc_kVpARtg0xz+WB01urGtsc+WeyBcKTXPHC6AWWVyLcw@mail.gmail.com"
type="cite"> However when I use 4 processors per replica that is
200 processors instead of 50 then the job runs fine without any
problem. <br>
</blockquote>
<br>
Probably that's just getting lucky with a starting configuration
that's still got some kind of problem. Without seeing .mdp files,
descriptions of simulation contents, preparation protocols and
actual series of command lines, we can't tell what. If you can take
the same .tpr files that sometimes cause problems with REMD, and
successfully use them in non-REMD simulations on a range of
differently-sized processor sets, then you might have evidence of a
problem - but the REMD code is stable and well tested by now.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CABUNsPc_kVpARtg0xz+WB01urGtsc+WeyBcKTXPHC6AWWVyLcw@mail.gmail.com"
type="cite">So I went back to the equilibrated systems described
in my first mail and used the nose hoover thermostat,
parinello-rahman semi-isotropic pressure coupling, coupled the
protein, lipid, water and ions separately with no velocity
generation and used 4 processors per replica and the simulation
runs fine. I had ran a 20 ns remd run and it has completed
successfully but for the exact same tpr files when I use 1
processor per replica I get the bad contacts error. Could the remd
crashing have been due to some scaling issue? if so, the error in
the log files with 'bad contacts' was misleading... <br>
<br>
Sheeba<br>
<br>
<br>
<br>
<br>
<br>
<div class="gmail_quote">On Wed, Jul 6, 2011 at 1:06 AM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff">
<div class="im"> On 6/07/2011 2:49 PM, Sheeba Jem wrote:
<blockquote type="cite"><br>
Hi Justin and Jianguo, <br>
<br>
Thank you for the suggestions. It makes sense to use the
same velocities from the equilibration output instead of
generating them and also to couple the groups
separately. However they dont seem to work. <br>
<br>
I changed the gen_vel to 0 and used the cpt files and
equilibration tpr files to generate the tpr files for
the replica exchange runs but still got the bad contacts
error. <br>
<br>
t = 2.010 ps: Water molecule starting at atom 21424 can
not be settled.<br>
Check for bad contacts and/or reduce the timestep.<br>
Wrote pdb files with previous and current coordinates<br>
Jul 5 23:10:10 2011 32736 4 7.04
handleTSRegisterTerm(): TS reports task <5> pid
<10337> on host<cmp-43-5> killed or core
dumped<br>
<br>
<br>
I generated the tpr files with the following command:<br>
<br>
/ifs1/apps/gromacs-405/bin/grompp -f remd.mdp -c
eq_1ns.tpr -o cptremd0.tpr -t eq_1ns.cpt -p popc_mlt.top
<br>
<br>
<br>
I then coupled the components of the system separately
and even that gave the same error.<br>
<br>
<br>
t = 2.018 ps: Water molecule starting at atom 7015 can
not be settled.<br>
Check for bad contacts and/or reduce the timestep.<br>
Wrote pdb files with previous and current coordinates<br>
Jul 6 00:13:11 2011 7377 4 7.04 handleTSRegisterTerm():
TS reports task <1> pid <24584> on
host<cmp-25-6> killed or core dumped<br>
<br>
I attach the mdp file that I used. I would appreciate
any other suggestions you might have. <br>
</blockquote>
<br>
</div>
The usual advice is here <a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up"
target="_blank">http://www.gromacs.org/Documentation/Terminology/Blowing_Up</a>.<br>
<br>
Give up on REMD until you get basic equilibration working.<br>
<font color="#888888"> <br>
Mark</font>
<div>
<div class="h5"><br>
<br>
<blockquote type="cite">Thanks<br>
<br>
Sheeba<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<div class="gmail_quote">On Tue, Jul 5, 2011 at 7:22
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 class="gmail_quote" style="margin: 0pt
0pt 0pt 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;">
<div><br>
<br>
Sheeba Jem wrote:<br>
<blockquote class="gmail_quote" style="margin:
0pt 0pt 0pt 0.8ex; border-left: 1px solid
rgb(204, 204, 204); padding-left: 1ex;"> <br>
Dear Gromacs users,<br>
<br>
I am having trouble running REMD for a system
containing one peptide molecule on the surface
of a lipid membrane, the system contains the
following:<br>
<br>
Protein 1<br>
POPC 128<br>
Water 4847<br>
Na+ 9<br>
Cl- 15<br>
<br>
The total number of atoms in the system is
21483. I have 50 replicas with temperatures
distributed from 250 to 400 K. After setting
up the system I minimized and equilibrated
the system for 14 ns at three temperatures:
250 K, 300K and 350 K. I take the output file
from the 250 K run and use that as the
starting structure for the temperatures
between 250 to 300 K; similarly the output
file from 300 K as the starting structure for
replicas between 300 to 350 K and for the
replicas between 350 to 400 K I use the output
from the 350 K run. I further equilibrate
these structures at the replica temperature
for 10 ns. The output from these 10 ns runs
are then used as starting structures for the
replica exchange simulation. However when the
replica exchange simulation begins to run, it
crashes after 2 ps with a bad contact error:<br>
<br>
</blockquote>
<br>
</div>
Your equilibration protocol doesn't make much
sense. First, you're not equilibrating properly
under all conditions, and then (in your .mdp file)
you're re-generating velocities so you just end up
destroying any equilibration you had previously
achieved. Membranes are particularly sensitive to
proper equilibration, so I suspect this is your
root problem. Equilibrate each system at the
desired temperature, maintaining the ensemble by
passing the appropriate .cpt file to grompp (with
"gen_vel = no" so as not to override the existing
velocities).
<div> <br>
<br>
<blockquote class="gmail_quote" style="margin:
0pt 0pt 0pt 0.8ex; border-left: 1px solid
rgb(204, 204, 204); padding-left: 1ex;"> <br>
t = 2.008 ps: Water molecule starting at atom
21421 can not be settled.<br>
Check for bad contacts and/or reduce the
timestep.<br>
Wrote pdb files with previous and current
coordinates<br>
Jul 4 18:07:21 2011 22666 4 7.04
handleTSRegisterTerm(): TS reports task
<7> pid <15856> on
host<cmp-13-9> killed or core dumped<br>
<br>
<br>
I use the Gromacs version 4.0.5 for all the
simulations. Since the starting structure for
each replica has been well equilibrated I am
not sure how there could be hard contacts in
the system. I looked at the <br>
</blockquote>
<br>
</div>
The configurations may be somewhat equilibrated,
but you're killing that by generating velocities.
<div><br>
<br>
<blockquote class="gmail_quote" style="margin:
0pt 0pt 0pt 0.8ex; border-left: 1px solid
rgb(204, 204, 204); padding-left: 1ex;"> input
structures and the trajectories from the
equilibration runs and I could not find
anything strange with the system leading to
hard contacts. Also the membrane remains
intact for the high temperature replicas.
Since I could not find anything to change in
the system, I tried running REMD reducing the
time step from 2 fs to 1 fs which also gave a
similar error:<br>
<br>
</blockquote>
<br>
</div>
If you get the same problem, it's likely still the
thermostatting/velocity generation that's the
problem.
<div><br>
<br>
<blockquote class="gmail_quote" style="margin:
0pt 0pt 0pt 0.8ex; border-left: 1px solid
rgb(204, 204, 204); padding-left: 1ex;"> t =
2.020 ps: Water molecule starting at atom
18919 can not be settled.<br>
Check for bad contacts and/or reduce the
timestep.<br>
Wrote pdb files with previous and current
coordinates<br>
<br>
I then tried with a timestep of 0.1 fs and got
the same bad contacts error:<br>
<br>
t = 0.101 ps: Water molecule starting at atom
20251 can not be settled.<br>
Check for bad contacts and/or reduce the
timestep.<br>
Wrote pdb files with previous and current
coordinates<br>
Jul 4 18:34:17 2011 25639 4 7.04
handleTSRegisterTerm(): TS reports task
<5> pid <17349> on
host<cmp-4-5> killed or core dumped<br>
<br>
<br>
I am not sure if reducing the timestep further
would help therefore I looked at the
temperature and pressure coupling. For all the
above simulations I had used nose-hoover
thermostat and a parrinello-rahman barostat
with semi-isotropic pressure coupling. I had
previously 'successfully' ran a REMD
simulation of the peptide in water with
isotropic coupling, the difference in the two
.mdp files were the type of pressure coupling
and changes in the bond contraint parameters
(I have attached both the mdp files). Since
semi-isotropic pressure coupling reproduces
membrane properties well, I had used it for
the peptide-lipid system. To see if changing
the coupling type made a difference, with the
0.1 fs time step, I changed the coupling type
to isotropic and this time the job crashed
with the lincs warning:<br>
<br>
</blockquote>
<br>
</div>
Membranes are more sensitive, especially to
temperature and pressure coupling and the state of
equilibration. Proteins in water are far more
robust and take a lot of beating before they
explode. Therefore, the comparison is not a
particularly good one. Apples and oranges.<br>
<br>
-Justin<br>
<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"
value="+15402319080" target="_blank">(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>
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<br>
-- <br>
with regards,<br>
I. Sheeba Jem.<br>
</blockquote>
<br>
</div>
</div>
</div>
<br>
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-- <br>
with regards,<br>
I. Sheeba Jem.<br>
</blockquote>
<br>
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