<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. However when I use 4 processors per replica that is 200 processors instead of 50 then the job runs fine without any problem. <br>
<br>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 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;">
<u></u>
<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 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></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 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 href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a 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>
<font color="#888888">
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</div>
<br>
<br clear="all">
<br>
-- <br>
with regards,<br>
I. Sheeba Jem.<br>
</blockquote>
<br>
</div></div></div>
<br>--<br>
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Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br><br clear="all"><br>-- <br>with regards,<br>I. Sheeba Jem.<br>