[gmx-users] REMD with 'bad contacts' error

[Sheeba Jem]

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:


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 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:

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:

Step 2112, time 0.2112 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 1741.123129, max 74557.351562 (between atoms 5726 and 5727)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5703   5704   46.5    0.1360   0.1954      0.1360
   5702   5703   88.3    0.1430   0.3582      0.1430
   5687   5688   92.2    0.1530   1.5410      0.1530
(a long list of angles..)


I then ran REMD with the same mdp file I had used for the peptide water
system changing only the temperature of the replicas accordingly and I still
got the bad contacts error:

t = 2.004 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  4 20:11:29 2011 31398 4 7.04 handleTSRegisterTerm(): TS reports task
<5> pid <26543> on host<cmp-23-1> killed or core dumped


I submit the REMD jobs with the following lines in a .lsf file

#!/bin/tcsh -f
#BSUB -J REMD
#BSUB -x
#BSUB -q 512cpu
#BSUB -n 50
#BSUB -e err.%J
#BSUB -o log.%J
#BSUB -a mvapich
mpirun /ifs1/apps/gromacs-405/bin/mdrun_mpi -s remd.tpr -multi 50 -replex
1000 -deffnm remd


I am not sure where I am going wrong  and any help is greatly appreciated.
Since the size of the mail is too big when I attach the files, the mail
bounces therefore I am sending only the input files used for the peptide
water system and the peptide lipid system.

Thank you

Sheeba
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110705/bb8033b7/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: remd_pep_lip.mdp
Type: application/octet-stream
Size: 1535 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110705/bb8033b7/attachment.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: remd_pep_water.mdp
Type: application/octet-stream
Size: 1360 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110705/bb8033b7/attachment-0001.obj>