From: Douglas Houston (DouglasR.Houston_at_ed.ac.uk)
Date: Thu Jun 19 2014 - 05:26:53 CDT
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.
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