<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>One thing you can try in your membrane simulation is to couple the Protein, Lipid and Water_Ion separately to the thermal bath.<br><br>Cheers,<br>Jianguo <br></div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Sheeba Jem <sheeba.jem@googlemail.com><br><b><span style="font-weight: bold;">To:</span></b> gmx-users@gromacs.org<br><b><span style="font-weight: bold;">Sent:</span></b> Wednesday, 6 July 2011 07:05:43<br><b><span style="font-weight: bold;">Subject:</span></b> [gmx-users] REMD with 'bad contacts' error<br></font><br><meta http-equiv="x-dns-prefetch-control"
content="off"><br>Dear Gromacs users,<br><br> 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:<br><br>Protein 1<br>POPC 128<br>Water 4847<br>
Na+ 9<br>Cl- 15<br><br>
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: <br>
<br><br>t = 2.008 ps: Water molecule starting at atom 21421 can not be settled.<br>Check for bad contacts and/or reduce the timestep.<br>Wrote pdb files with previous and current coordinates<br>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<br>
<br><br>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:<br>
<br>t = 2.020 ps: Water molecule starting at atom 18919 can not be settled.<br>Check for bad contacts and/or reduce the timestep.<br>Wrote pdb files with previous and current coordinates<br><br>I then tried with a timestep of 0.1 fs and got the same bad contacts error:<br>
<br>t = 0.101 ps: Water molecule starting at atom 20251 can not be settled.<br>Check for bad contacts and/or reduce the timestep.<br>Wrote pdb files with previous and current coordinates<br>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<br>
<br><br>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:<br>
<br>Step 2112, time 0.2112 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 1741.123129, max 74557.351562 (between atoms 5726 and 5727)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br>
5703 5704 46.5 0.1360 0.1954 0.1360<br> 5702 5703 88.3 0.1430 0.3582 0.1430<br> 5687 5688 92.2 0.1530 1.5410 0.1530<br>(a long list of angles..)<br><br><br>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:<br>
<br>t = 2.004 ps: Water molecule starting at atom 21424 can not be settled.<br>Check for bad contacts and/or reduce the timestep.<br>Wrote pdb files with previous and current coordinates<br>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<br>
<br><br>I submit the REMD jobs with the following lines in a .lsf file<br><br>#!/bin/tcsh -f<br>#BSUB -J REMD<br>#BSUB -x<br>#BSUB -q 512cpu<br>
#BSUB -n 50<br>#BSUB -e err.%J <br>#BSUB -o log.%J <br>#BSUB -a mvapich <br>mpirun /ifs1/apps/gromacs-405/bin/mdrun_mpi -s remd.tpr -multi 50 -replex 1000 -deffnm remd<br><br><br>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. <br>
<br>Thank you<br><br>Sheeba<br><br>
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