[gmx-users] step 0Segmentation fault
ram bio
rmbio861 at gmail.com
Wed Oct 7 11:55:15 CEST 2009
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
editconf -f protein_processed.gro -o protein_newbox.gro -c -box
6.41840 6.44350 6.59650 -rotate 0 0 90
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
cat protein_newbox.gro dppc128.gro > system1.gro
I also used various box types like dodecahedron , octahedron but was
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.
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
>>>>>> 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
>>>>>
>>>>> ========================================
>>>>> _______________________________________________
>>>>> 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
>>>
>>> ========================================
>>> _______________________________________________
>>> 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
> Please search the archive at http://www.gromacs.org/search before posting!
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