[gmx-users] step 0Segmentation fault
ram bio
rmbio861 at gmail.com
Tue Oct 6 13:39:22 CEST 2009
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
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 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
>>>> _______________________________________________
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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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