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

[Jianguo Li]

One thing you can try in your membrane simulation is to couple the Protein, 
Lipid and Water_Ion separately to the thermal bath.

Cheers,
Jianguo 




________________________________
From: Sheeba Jem <sheeba.jem at googlemail.com>
To: gmx-users at gromacs.org
Sent: Wednesday, 6 July 2011 07:05:43
Subject: [gmx-users] REMD with 'bad contacts' error


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
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