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

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jul 6 07:06:20 CEST 2011


On 6/07/2011 2:49 PM, Sheeba Jem wrote:
>
> Hi Justin and Jianguo,
>
> Thank you for the suggestions. It makes sense to use the same 
> velocities from the equilibration output instead of generating them 
> and also to couple the groups separately. However they dont seem to work.
>
> I changed the gen_vel to 0 and used the cpt files and equilibration 
> tpr files to generate the tpr files for the replica exchange runs but 
> still got the bad contacts error.
>
> t = 2.010 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  5 23:10:10 2011 32736 4 7.04 handleTSRegisterTerm(): TS reports 
> task <5> pid <10337> on host<cmp-43-5> killed or core dumped
>
>
> I generated the tpr files with the following command:
>
> /ifs1/apps/gromacs-405/bin/grompp -f remd.mdp -c eq_1ns.tpr -o 
> cptremd0.tpr -t eq_1ns.cpt -p popc_mlt.top
>
>
> I then coupled the components of the system separately and even that 
> gave the same error.
>
>
> t = 2.018 ps: Water molecule starting at atom 7015 can not be settled.
> Check for bad contacts and/or reduce the timestep.
> Wrote pdb files with previous and current coordinates
> Jul  6 00:13:11 2011 7377 4 7.04 handleTSRegisterTerm(): TS reports 
> task <1> pid <24584> on host<cmp-25-6> killed or core dumped
>
> I attach the mdp file that I used. I would appreciate any other 
> suggestions you might have.

The usual advice is here 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up.

Give up on REMD until you get basic equilibration working.

Mark

> Thanks
>
> Sheeba
>
>
>
>
>
>
>
>
>
> On Tue, Jul 5, 2011 at 7:22 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     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 <http://vt.edu> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
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>
>
> -- 
> with regards,
> I. Sheeba Jem.

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