[gmx-users] step 0Segmentation fault

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 6 12:42:51 CEST 2009

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.


> 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


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