[gmx-users] step 0Segmentation fault
Justin A. Lemkul
jalemkul at vt.edu
Tue Oct 6 14:09:07 CEST 2009
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
>>>>> _______________________________________________
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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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>> --
>> ========================================
>>
>> 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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>
--
========================================
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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