On 15/07/2011 12:40 AM, Sheeba Jem wrote:
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.
How soon? Under what REMD regime? The volume scaling required for NPT
REMD can occasionally be problematic.
However when I use 4 processors per replica that is 200 processors
instead of 50 then the job runs fine without any problem.
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.
Mark
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...
Sheeba
On Wed, Jul 6, 2011 at 1:06 AM, Mark Abraham <[email protected]
<mailto:[email protected]>> wrote:
On 6/07/2011 2:49 PM, Sheeba Jem wrote:
Hi Justin and Jianguo,
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.
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.
t = 2.010 ps: Water molecule starting at atom 21424 can not be
settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
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
I generated the tpr files with the following command:
/ifs1/apps/gromacs-405/bin/grompp -f remd.mdp -c eq_1ns.tpr -o
cptremd0.tpr -t eq_1ns.cpt -p popc_mlt.top
I then coupled the components of the system separately and even
that gave the same error.
t = 2.018 ps: Water molecule starting at atom 7015 can not be
settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
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
I attach the mdp file that I used. I would appreciate any other
suggestions you might have.
The usual advice is here
http://www.gromacs.org/Documentation/Terminology/Blowing_Up.
Give up on REMD until you get basic equilibration working.
Mark
Thanks
Sheeba
On Tue, Jul 5, 2011 at 7:22 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Sheeba Jem wrote:
Dear Gromacs users,
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:
Protein 1
POPC 128
Water 4847
Na+ 9
Cl- 15
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:
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).
t = 2.008 ps: Water molecule starting at atom 21421 can
not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
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
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
The configurations may be somewhat equilibrated, but you're
killing that by generating velocities.
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:
If you get the same problem, it's likely still the
thermostatting/velocity generation that's the problem.
t = 2.020 ps: Water molecule starting at atom 18919 can
not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
I then tried with a timestep of 0.1 fs and got the same
bad contacts error:
t = 0.101 ps: Water molecule starting at atom 20251 can
not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
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
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:
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.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
with regards,
I. Sheeba Jem.
--
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
with regards,
I. Sheeba Jem.
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
