[gmx-users] segmentation fault with lincs warning
Justin A. Lemkul
jalemkul at vt.edu
Mon Jul 21 14:41:20 CEST 2008
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ANINDITA GAYEN wrote:
>
> dear sir,
>
>
>
> I have tried to insert only one chaps in the bilayer and the problem arose after the minimisation when i started the MD. I have also tried to do a minimistaion using lincs, where the minimisation also failed to proceed. Can you please tell me is this shows that the topology is broken and therefore it cannot produce the actual geometry?
>
As I said before, EM is not guaranteed to remove all bad contacts. If your
minimization fails with LINCS warnings, it is most likely due to the fact that
you have bad steric clashes. Check the atom pairs that LINCS prints it; it will
give you a clue as to where the problem lies.
Other options include removing a different lipid; maybe the location you've
selected is a bad one to try to disturb the bilayer.
> I am also trying to take a last chance where i want to use the genbox command to place the chaps in the bilyer. But, one of my colleague have faced a problem that inserting one protein in a bilayer caused removal of about 9 lipid molecules. Will this cause a problem in the original bilayer property?
>
Well, what do you expect? If you need to place a large molecule in the bilayer,
several lipids may have to be removed :)
Sufficient equilibration (tens of ns under the appropriate conditions) should
return bilayer properties to normal. Only after this time should you begin data
collection. "Solvating" a single CHAPS molecule with your bilayer should not
remove too many lipids, probably just one or two.
> I am disturbing a number of times; but i am really helpless. If the minimisation with lincs fails for a molecule, i want to know is the topology totally incorrect? Then what shall i do?
>
Without seeing the topology, I have no idea. But that's not my job, or anyone's
on the list. You've got to check your own work.
-Justin
> Can anyone please help me with the topology?
>
>
> --- On Mon, 21/7/08, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>> From: Justin A. Lemkul <jalemkul at vt.edu>
>> Subject: Re: [gmx-users] segmentation fault with lincs warning
>> To: aninditagayen at yahoo.co.in
>> Cc: gmx-users at gromacs.org
>> Date: Monday, 21 July, 2008, 6:26 AM
>> ANINDITA GAYEN wrote:
>>> Dear Sir,
>>>
>>> I have removed now one dmpc molecule from the
>> bilayer, but the problem is the same. I have also tried
>> using a downloaded pdb of chaps from pdb data bank, i.e.
>> 1XU9. Why all the bonds of chaps are rotating more than 30
>> degree when i have already minimised chaps to a reasonable
>> potential value? Is there any problem in the topology?
>> "Is the topology broken?" i have read that this
>> type of problem may happen if i have problem in my topology
>> file. This can be true as i have built the topology by hand
>> using the toplogy file from prodrg2 server and oplsaa force
>> field bonds, angles, and dihedrals.
>> It sounds like your in vacuo minimization was successful,
>> so I doubt that your
>> topology is severely broken. There are plenty of pitfalls
>> in converting a
>> GROMOS topology from PRODRG to OPLS-AA, but I recall
>> several discussions on this
>> topic a while back, so my comments are the same as those
>> I've already given.
>>
>>> Can you tell me what will be the rpoblem if i use
>> oplsUA atom descriptions for chaps? Are OPLSUA atom and
>> geometry definintion that are defined in the OPPLSAA itp
>> files in the gromacs ff library totally uncompatible with
>> OPLSAA?
>> I know nothing about OPLS-UA, but my knee-jerk reaction to
>> this question is
>> "absolutely not." One cannot represent, say,
>> nonbonded interactions under (for
>> example) OPLS-UA, then apply bonded parameters from
>> OPLS-AA, or vice versa, or
>> some hybrid of both.
>>
>> I don't think that messing with the force field
>> representation of CHAPS is going
>> to substantially change things.
>>
>>> If yes, then what is the way? how can i insert chaps
>> in the bilayer?
>> Alright, so you removed one lipid from your DMPC bilayer,
>> but that does not
>> guarantee that all steric clashes are resolved. Are you
>> still trying to fit 4
>> CHAPS into the bilayer, as in your quoted message below, or
>> just one molecule?
>> The latter case would probably be the best one.
>>
>> Also, is this crash occurring during minimization,
>> equilibration, or MD? Be
>> aware also that even if you pass through minimization, not
>> all unfavorable
>> clashes will necessarily be resolved by energy
>> minimization. EM just provides a
>> "reasonable" starting structure for the
>> simulation.
>>
>> If manual removal of a single DMPC does not allow for
>> appropriate insertion of
>> CHAPS, try another methodology, such as using genbox or
>> InflatGRO to prepare the
>> input structure.
>>
>> -Justin
>>
>>> Sincerely
>>> yours,
>>> Anindita Gayen
>>>
>>>
>>> --- On Mon, 14/7/08, Justin A. Lemkul
>> <jalemkul at vt.edu> wrote:
>>>> From: Justin A. Lemkul <jalemkul at vt.edu>
>>>> Subject: Re: [gmx-users] segmentation fault with
>> lincs warning
>>>> To: aninditagayen at yahoo.co.in, "Discussion
>> list for GROMACS users" <gmx-users at gromacs.org>
>>>> Date: Monday, 14 July, 2008, 4:40 PM
>>>> ANINDITA GAYEN wrote:
>>>>> Dear all,
>>>>>
>>>>>
>>>>> I have an dmpc bilayer equilibrated for 12 ns.
>> I have
>>>> built a CHAPS molecule in the OPLSAA force field
>> and
>>>> inserted it in the equilibrated bilayer. There was
>> no
>>>> problem till the minimisation, but when i started
>> the MD,
>>>> the job escaped out with a lincs error
>>>>> Initializing LINear Constraint Solver
>>>>> number of constraints is 6572
>>>>> average number of constraints coupled to one
>>>> constraint is 3.3
>>>>> Rel. Constraint Deviation: Max between
>> atoms
>>>> RMS
>>>>> Before LINCS 0.817519 4126
>> 4128
>>>> 0.017115
>>>>> After LINCS 30.145958 17066
>> 17068
>>>> 1.789056
>>>>> Step -2, time -0.004 (ps) LINCS WARNING
>>>>> relative constraint deviation after LINCS:
>>>>> max 30.145958 (between atoms 17066 and 17068)
>> rms
>>>> 1.789056
>>>>> bonds that rotated more than 30 degrees:
>>>>> atom 1 atom 2 angle previous, current,
>> constraint
>>>> length
>>>>> 4128 4129 31.1 0.1571 0.1600
>> 0.1530
>>>>> 16859 16858 36.1 0.1529 0.1022
>> 0.1529
>>>>> 16858 16859 36.1 0.1529 0.1022
>> 0.1529
>>>>> 16897 16858 49.2 0.1523 0.1495
>> 0.1529
>>>>> [all the atoms and bonds in the error list are
>> for
>>>> CHAPS]
>>>>> Do i have the problem in the topology file? I
>> have
>>>> inserted 4 chaps mole cules without replacing the
>> dmpc
>>>> molecules, i.e. 4 chaps with 128 dmpc molecules in
>> the
>>>> bilayer. Is this causing any steric problem?
>>>> This is a *very* common problem, and a lot of
>> potential
>>>> solutions are in the
>>>> list archive and wiki site. As such, I won't
>> list them
>>>> here, but you can
>>>> certainly find them within a few minutes (or
>> seconds) of
>>>> searching.
>>>>
>>>> If you have a pre-equilibrated bilayer, and
>> inserted
>>>> molecules into it without
>>>> removing any lipids, you probably have very severe
>> atomic
>>>> overlap. But as I
>>>> said, search the archive and try the things you
>> find there.
>>>> -Justin
>>>>
>>>>> Please suggest a way to get out of the
>> problem. If you
>>>> want, i can upload my topology and mdp files in
>> the next
>>>> mail.
>>>>> Yours truly,
>>>>> anindita gayen
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Unlimited freedom, unlimited storage.
>> Get it
>>>> now, on
>>>>
>> http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/
>> _______________________________________________
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>>>> --
>>>> ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Graduate Research Assistant
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>> ========================================
>>>
>>> Bring your gang together. Do your thing. Find
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>>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>
>
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>
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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