[gmx-users] step 0Segmentation fault
Justin A. Lemkul
jalemkul at vt.edu
Wed Oct 7 12:36:10 CEST 2009
ram bio wrote:
> Dear Justin,
>
> Thanks for the options suggested.
>
> I have used -princ and rotate 0 0 90 options with editconf and was
> able to place the protein vertically and at the centre of the DPPC
> bilayer (128 + 3655) from the site provided in the tutorial, but still
> the part of protein is outside the DPPC layer (examined system.gro
> (protein newbox +dppc128.gr0) in VMD). The commands used were
>
This isn't necessarily a problem. So your protein sticks out - that will
probably be the case in most membrane protein systems.
> editconf -f protein_processed.gro -o protein_newbox.gro -c -box
> 6.41840 6.44350 6.59650 -rotate 0 0 90
>
Depending on the degree to which the protein is protruding out of the bilayer,
you may have to adjust the z dimension of the box, as I've suggested before.
> cat protein_newbox.gro dppc128.gro > system.gro
>
>
> so now, i tried to increase the size of the box by redoing it and
> using the command
>
> editconf -f protein_processed.gro -o protein_newbox.gro -c -box
> 6.41840 6.44350 6.59650 -d 1.0 -rotate 0 0 90 -bt cubic
>
I don't know what effect this will have. It is contradictory to specify a
non-cubic box by assigning the vectors explicitly, then using -bt cubic. I
doubt you're getting what you think you are, but I don't know which option has
precendence, -box or -bt. Either way, you're not doing anything to increase the
box size. Also note that the box size in dppc128.gro would have to be similarly
manipulated to actually get a larger box.
> cat protein_newbox.gro dppc128.gro > system1.gro
>
> I also used various box types like dodecahedron , octahedron but was
These boxes make no sense for a square cross-section of a membrane.
> unable increase the size of the box and fix the protein in the centre
> of the dppcbilayer (128 + 3655 H2O). Please suggest me how to correct
> my command so that all the protein lies in the dppcbilayer and is in
> the centre and can proceed to inflategro steps, also do i need to use
> a dppclayer with more lipids like 256 lipid bilayer.
Well, using editconf properly will help. Define a proper box with -box, don't
just keep copying the one I use in the tutorial. The x and y components may
stay the same, but you may have to increase the z vector.
The same process applies with any bilayer, even if it has 256 lipids.
-Justin
>
> Thanks,
>
> Ram
>
> On Tue, Oct 6, 2009 at 5:39 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> ram bio wrote:
>>> Dear Justin,
>>>
>>> As suggested, when i reexamined the system.gro (protein_newbox +
>>> dppc128) one of the ends of the problem (as i think) i.e. few
>>> aminoacids of protein were beyond the water surface of the bilayer,
>>> probably this may be the reason for the presence of water molecules to
>>> the side of the bilayer when solvated and also lack of minimization
>>> during inflategro step. One more thing, I am inserting the protein in
>> Indeed, if your system doesn't actually fit within the unit cell you've
>> defined, you're in for trouble. Always look at your output!
>>
>>> lipid bilayer by orienting it using your KALP peptide (.pdb) as
>>> reference in VMD and later using editconf to centre the protein using
>>> option i.e. -c -box 6.41840 6.44350 6.59650, otherwise if i just use
>>> editconf command, it is orienting horizontally instead of vertically,
>> I don't fully understand what you're doing. You also may not be able to use
>> the exact same box that I defined in the tutorial (the original DPPC box).
>> If you've got pieces of your protein protruding out of the unit cell, then
>> you'll need to define a suitably-sized box. Horizontal vs. vertical issues
>> can be solved by editconf -rotate.
>>
>> -Justin
>>
>>> i can do the orientation manually using vmd but it is difficult and
>>> iam unable to orient it exactly in the centre and vertical in the dppc
>>> bilayer.
>>>
>>> Please suggest some corrections as I am going to reorient and position
>>> it in the bilayer and redo the inflategro procedure.
>>>
>>> Thanks
>>>
>>> Ram
>>>
>>> On Tue, Oct 6, 2009 at 4:42 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>>> ram bio wrote:
>>>>> Dear Justin,
>>>>>
>>>>> Thanks for the advice. I am using the DPPC 128 lipid bilayer from D.
>>>>> Peter Tieleman website, and the nvt.mdp file and the nvt.log files are
>>>>> as follows as in your tutorial:
>>>> <snip>
>>>>
>>>>> Constraining the starting coordinates (step 0)
>>>>>
>>>>> Constraining the coordinates at t0-dt (step 0)
>>>>> RMS relative constraint deviation after constraining: 9.42e-04
>>>>> Initial temperature: 503.557 K
>>>>>
>>>>> Started mdrun on node 0 Thu Jun 25 11:30:30 2009
>>>>>
>>>>> Step Time Lambda
>>>>> 0 0.00000 0.00000
>>>>>
>>>>> Grid: 9 x 9 x 9 cells
>>>>> Large VCM(group Protein_DPPC): -50.08205, 97.99061,
>>>>> 16.32530, Temp-cm: 2.50669e+05
>>>>> Long Range LJ corr.: <C6> 2.0307e-03
>>>>> Long Range LJ corr.: Epot -1862.02, Pres: -184.12, Vir: 1862.02
>>>>> Energies (kJ/mol)
>>>>> Angle G96Angle Proper Dih. Ryckaert-Bell. Improper
>>>>> Dih.
>>>>> 1.48814e+04 8.19090e+03 8.43857e+03 6.38969e+03
>>>>> 2.93352e+03
>>>>> LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb
>>>>> (SR)
>>>>> 4.09831e+03 5.49186e+04 7.87055e+09 -1.86202e+03
>>>>> -1.48414e+05
>>>>> Coul. recip. Position Rest. Potential Kinetic En. Total
>>>>> Energy
>>>>> -1.53985e+05 9.50084e+00 7.87034e+09 3.08099e+17
>>>>> 3.08099e+17
>>>>> Conserved En. Temperature Pressure (bar) Cons. rmsd ()
>>>>> 3.08099e+17 2.31982e+15 1.01551e+16 7.25066e+04
>>>>>
>>>> The information shown here indicates very strongly that you have severe
>>>> atomic overlap in your starting structure. This is probably from the
>>>> InflateGRO minimization that did not converge appropriately. Your
>>>> potential
>>>> energy is astronomically high, as well as factors like temperature, and
>>>> thus
>>>> kinetic energy. The latter are related to trying to constrain an
>>>> inappropriate starting structure.
>>>>
>>>> I would suggest going back to the initial construction stage, figuring
>>>> out
>>>> why that minimization didn't converge, and start over from there.
>>>> Plowing
>>>> ahead when you get unfavorable results is a recipe for LINCS warnings.
>>>>
>>>> -Justin
>>>>
>>>>> Please diagnose the information and suggest.
>>>>>
>>>>> Thanks
>>>>>
>>>>> ram
>>>>>
>>>>>
>>>>> On Tue, Oct 6, 2009 at 4:12 PM, Justin A. Lemkul <jalemkul at vt.edu>
>>>>> wrote:
>>>>>> ram bio wrote:
>>>>>>> Dear Gromacs Users,
>>>>>>>
>>>>>>> I have inserted the protein in lipid bilayer and performed Inflategro
>>>>>>> I am able to reach the required area per lipid after certain
>>>>>>> iterations but was unable to get the standard Epot and Fmax values
>>>>>>> that is negative and to the power of 5 or 6 and Fmax less than 1000
>>>>>> You won't get that magnitude of Epot without water. If you can't reach
>>>>>> Fmax
>>>>>> < 1000, you shouldn't just plow ahead. Analyze where the problem is,
>>>>>> because it is unlikely to go away by magic!
>>>>>>
>>>>>>> during the last minimization , later i solvated the protein using a
>>>>>>> vanderwaal radii for carbon as 0.375, i found some water molecules not
>>>>>>> in the core of the lipid layer but to the sides, as they were not in
>>>>>>> the centre i ionated the complex with 13 chloride ions as the charge
>>>>>> Did you get rid of these waters? You can always try tweaking the entry
>>>>>> in
>>>>>> vdwradii.dat for C. As far as those on the sides are concerned, it
>>>>>> sounds
>>>>>> like the box you've created is too large for the lipids. I wouldn't
>>>>>> use
>>>>>> this system, because you'll waste a huge amount of time hoping it
>>>>>> equilibrates right.
>>>>>>
>>>>>>> shown was non-zero total intergral charge 1.30000e+01, then i minized
>>>>>>> the ionized complex with the minim.mdp file in as per justin tutorial,
>>>>>>> i am following all the mdp files as per the tutorial till now, and was
>>>>>>> able to obtain Potential Energy = -1.8947278e+05
>>>>>>> Maximum force = 9.1642163e+02 on atom 7647
>>>>>>> Norm of force = 5.0845932e+01
>>>>>>>
>>>>>> That looks fine, but I still think there is an underlying problem in
>>>>>> your
>>>>>> InflateGRO construction step.
>>>>>>
>>>>>>> and then i created the index file ane while running the nvt
>>>>>>> equilllibrqtion i am getting
>>>>>>>
>>>>>>> Step 0, time 0 (ps) LINCS WARNING
>>>>>>> relative constraint deviation after LINCS:
>>>>>>> rms 0.007117, max 0.443345 (between atoms 6311 and 6312)
>>>>>>> bonds that rotated more than 30 degrees:
>>>>>>> atom 1 atom 2 angle previous, current, constraint length
>>>>>>>
>>>>>> The classic case of "blowing up." See either my Advanced
>>>>>> Troubleshooting
>>>>>> page in the tutorial, or
>>>>>> http://www.gromacs.org/Documentation/Terminology/Blowing_Up. If you
>>>>>> want
>>>>>> more specific advice, you'll have to provide information at least about
>>>>>> what
>>>>>> type of lipid you're using, and what you have in your .mdp file.
>>>>>>
>>>>>>> Can any body suggest me how to rectify the defect and is it the
>>>>>>> problem with compliation as i am using gromacs 4.0.3 or the memory
>>>>>>> space or my running the job.
>>>>>> Well, first off I'd recommend always using the most current version of
>>>>>> the
>>>>>> software, not that it's likely to impact your system, but just in
>>>>>> general.
>>>>>> This is a problem reported to this list almost daily, so please also
>>>>>> check
>>>>>> the archives. There are literally thousands of posts regarding LINCS
>>>>>> warnings and unstable systems.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>> Thanks
>>>>>>>
>>>>>>> Ram
>>>>>>> _______________________________________________
>>>>>>> gmx-users mailing list gmx-users at gromacs.org
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>>>>>>>
>>>>>> --
>>>>>> ========================================
>>>>>>
>>>>>> Justin A. Lemkul
>>>>>> Ph.D. Candidate
>>>>>> ICTAS Doctoral Scholar
>>>>>> Department of Biochemistry
>>>>>> Virginia Tech
>>>>>> Blacksburg, VA
>>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>>>
>>>>>> ========================================
>>>>>> _______________________________________________
>>>>>> gmx-users mailing list gmx-users at gromacs.org
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>>>>>>
>>>> --
>>>> ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Ph.D. Candidate
>>>> ICTAS Doctoral Scholar
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>> ========================================
>>>> _______________________________________________
>>>> gmx-users mailing list gmx-users at gromacs.org
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>>>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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