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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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