From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Sat Jun 21 2014 - 18:43:43 CDT
Let me see if I understand how you've put this together...
You've got your special "linker" residue OL1 which is a 10-carbon chain with a peptide backbone on each end, and a methyl group in place of the alpha hydrogen. It's effectively symmetrical, but you've got one end defined as the "backbone" and inserted as resid 3038, and are patching the other end in between 3045 and 3047. So I take it...
"patch DELB" deletes the existing amide bond between 3045 and 3047; "patch STCN" makes a new amide bond between 3045 and 3038; patch STNC makes the bond between 3038 and 3047... what does CMPS do?
I'll let someone more knowledgeable than me comment on the behaviour you're seeing... but may I suggest an easier way to get to the same end goal? Why not chop your OL1 residue in half? Define it as simply a (C-alpha) methylated amino acid with a linear 5-carbon sidechain, and insert a copy at positions 3038 and 3046. Then it's one very simple patch to link the two copies together at their terminal carbons. The fewer (and simpler) patches you introduce, the less likely you are to introduce problems - and those problems you do introduce will be easier to troubleshoot.
Cheers,
Tristan
-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Douglas Houston
Sent: Friday, 20 June 2014 11:32 PM
To: Aron Broom
Cc: Namd Mailing List
Subject: Re: namd-l: Constraint failure in RATTLE algorithm
Hi Aron,
Thanks, this allows me to reproduce the problem. The following files
should be enough for anyone to visualise the instability:
https://drive.google.com/file/d/0B3IbJv_UNHlWN3p0bTR6NjFER2M/edit?usp=sharing
https://drive.google.com/file/d/0B3IbJv_UNHlWYXYwYkZCTmkzc2M/edit?usp=sharing
https://drive.google.com/file/d/0B3IbJv_UNHlWQmlfTjhoNjZUZWc/edit?usp=sharing
Apart from the problem atoms flying around, I notice the whole system
is "pulsing" - is this normal or indicative of a problem with e.g.
pressure?
cheres,
Doug
Quoting Aron Broom <broomsday_at_gmail.com> on Thu, 19 Jun 2014 11:37:59 -0400:
> 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
>
_____________________________________________________
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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