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
remd_pep_lip.mdp
Description: Binary data
remd_pep_water.mdp
Description: Binary data
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