From: Aron Broom (broomsday_at_gmail.com)
Date: Thu Jun 19 2014 - 10:37:59 CDT
You'd just need to save that frame's coordinates using VMD, and then use
those as an input for a "new" simulation. But of course don't do any
minimization.
On Thu, Jun 19, 2014 at 10:51 AM, Douglas Houston <DouglasR.Houston_at_ed.ac.uk
> wrote:
> Hi Aron,
>
> I had considered starting from just before where the distortion sets in
> but wasn't sure how to do that?
>
> As I understand it the "firsttimestep" keyword doesn't specify the frame
> to start on, merely where to start the numbering. Is there another keyword
> I need to use to get the simulation to start from a particular frame?
>
> cheers,
> Doug
>
>
>
>
> Quoting Aron Broom <broomsday_at_gmail.com> on Thu, 19 Jun 2014 10:15:49
> -0400:
>
> 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
>>
>>
>
>
>
> _____________________________________________________
> 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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