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
========================================
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--
with regards,
I. Sheeba Jem.
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