[gmx-users] REMD with 'bad contacts' error
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Jul 14 19:15:23 CEST 2011
On 15/07/2011 12:40 AM, Sheeba Jem wrote:
>
> Hi, I had been trying different thermostats, barostats, time steps and
> coupling times to get remd for the peptide lipid system working and I
> had even equilibrated each replica for 50 ns before submitting them to
> remd. However none of them work when I use one processor per replica.
> That is, I have 50 replicas and when I submit the job with 50
> processors the job crashes with the bad contacts error.
How soon? Under what REMD regime? The volume scaling required for NPT
REMD can occasionally be problematic.
> However when I use 4 processors per replica that is 200 processors
> instead of 50 then the job runs fine without any problem.
Probably that's just getting lucky with a starting configuration that's
still got some kind of problem. Without seeing .mdp files, descriptions
of simulation contents, preparation protocols and actual series of
command lines, we can't tell what. If you can take the same .tpr files
that sometimes cause problems with REMD, and successfully use them in
non-REMD simulations on a range of differently-sized processor sets,
then you might have evidence of a problem - but the REMD code is stable
and well tested by now.
Mark
> So I went back to the equilibrated systems described in my first mail
> and used the nose hoover thermostat, parinello-rahman semi-isotropic
> pressure coupling, coupled the protein, lipid, water and ions
> separately with no velocity generation and used 4 processors per
> replica and the simulation runs fine. I had ran a 20 ns remd run and
> it has completed successfully but for the exact same tpr files when I
> use 1 processor per replica I get the bad contacts error. Could the
> remd crashing have been due to some scaling issue? if so, the error in
> the log files with 'bad contacts' was misleading...
>
> Sheeba
>
>
>
>
>
> On Wed, Jul 6, 2011 at 1:06 AM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
> 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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>
>
> --
> with regards,
> I. Sheeba Jem.
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