From: Aron Broom (broomsday_at_gmail.com)
Date: Thu Jun 19 2014 - 09:15:49 CDT
You're right Normal, I did also mean DCDFreq.
Douglas,
What happens if you take your "penultimate frame" and restart from that,
does it fail again very quickly?
I agree that if it's taking any more than a few ps to crash, minimization
likely isn't the problem. It sounds like there is a very sensitive problem
that only appears under specific circumstances, maybe something with a
dihedral.
~Aron
On Thu, Jun 19, 2014 at 6:26 AM, Douglas Houston <DouglasR.Houston_at_ed.ac.uk>
wrote:
> Hi all,
>
> Thanks for all the suggestions. A few more details:
>
> This is not particularly reproducible. The error may occur after 5ns or
> 50ns. I have been running 20ns simulations and usually they finish, but now
> I want to do a 200ns simulation.
>
> When I visualise the trajectory just before the failure I see that the
> residue the atom belongs to (3045) is heavily distorted in the final frame;
> it looks OK in the penultimate frame. I will rerun with smaller dcdfreq as
> Norman suggested. I will also increase the timestep from 0.5 to 2 fs as
> this will hopefully throw the error sooner (my current simulation failed
> after 3 days of running).
>
> I do 10,000 minimization steps to start. The fact that the system is
> stable for up to 50ns suggests to me that further initial minimization
> won't help ... ?
>
> I understand that I may well have have a problem with bad parameters, or a
> bad/incomplete topology. Residue 3045 has a number of patches applied to
> it.
>
> The following lists the psfgen commands I have been using to generate the
> topology:
>
> package require psfgen
> topology top_all36_prot_ole.rtf
> topology top_all36_lipid.rtf
> topology toppar_water_ions.str
> pdbalias residue HIS HSE
> pdbalias atom ILE CD1 CD
> segment A {pdb 5CstapleW2A.pdb
> first ACE
> last CT2}
> patch DELB A:3045 A:3047
> patch STCN A:3045 A:3038
> patch STNC A:3038 A:3047
> patch CMPS A:3045 A:3038 A:3047
> coordpdb 5CstapleW2A.pdb A
> regenerate angles dihedrals
> guesscoord
> writepdb 5CstapleW2A_psfgen.pdb
> writepsf 5CstapleW2A_psfgen.psf
>
>
>
>
>
> Quoting Axel Kohlmeyer <akohlmey_at_gmail.com> on Wed, 18 Jun 2014 14:23:05
> -0400:
>
> On Wed, Jun 18, 2014 at 1:29 PM, Douglas Houston
>> <DouglasR.Houston_at_ed.ac.uk> wrote:
>>
>>> Hi all,
>>>
>>> I keep encountering the following fatal error:
>>>
>>> ERROR: Constraint failure in RATTLE algorithm for atom 189!
>>> ERROR: Constraint failure; simulation has become unstable.
>>> ERROR: Exiting prematurely; see error messages above.
>>>
>>> The atom itself varies. I have searched previous messages and tried the
>>> suggestions (smaller timestep, minimization overkill, etc.) to no avail.
>>>
>>> What else could I try to get my simulation to finish? I have attached my
>>>
>>
>> you need to look at this from a different perspective. first you need
>> to find out the reason, not try to suppress it.
>>
>> how reproducible is this failure? how soon does this happen after the
>> start of your simulation. have you visualized your simulation around
>> the time of the failure and seen where exactly an atom experiences
>> (too) large forces. you may have a problem with bad parameters, or a
>> bad/incomplete topology (= .psf) file. or you are very very far away
>> from equilibrium and may need to do multiple iterations of
>> minimization and relaxation. and so on and so on. there are many ways,
>> but no simple general solution that works always.
>>
>> axel.
>>
>>
>> .conf file so you can see my system and the simulation parameters I am
>>> specifying.
>>>
>>
>>
>>
>> cheers,
>>> Doug
>>>
>>> _____________________________________________________
>>> Dr. Douglas R. Houston
>>> Lecturer
>>> Institute of Structural and Molecular Biology
>>> Room 3.23, Michael Swann Building
>>> King's Buildings
>>> University of Edinburgh
>>> Edinburgh, EH9 3JR, UK
>>> Tel. 0131 650 7358
>>> http://tinyurl.com/douglasrhouston
>>>
>>>
>>> --
>>> The University of Edinburgh is a charitable body, registered in
>>> Scotland, with registration number SC005336.
>>>
>>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>>
>>
>
>
>
> _____________________________________________________
> Dr. Douglas R. Houston
> Lecturer
> Institute of Structural and Molecular Biology
> Room 3.23, Michael Swann Building
> King's Buildings
> University of Edinburgh
> Edinburgh, EH9 3JR, UK
> Tel. 0131 650 7358
> http://tinyurl.com/douglasrhouston
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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