[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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