[gmx-users] segmantation default

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 1 18:41:17 CET 2012

mehmet kıytak wrote:
> hi all...
> ı have a problem.. ı got segmentation fault when run nvt equilibration.. 
> ı use below mdp file

Please post a complete .mdp file.  The Unix 'cat' command can be used to print 
the contents of the text file, which can then be copied and pasted into an email.

> couple-lambda0           = vdw      ; only van der Waals interactions
> couple-lambda1           = none     ; turn off everything, in this case 
> only vdW
> couple-intramol          = no
> nstdhdl                  = 10

It appears you are trying to do a free energy calculation by transforming your 
system.  Turn off the free energy code to determine whether or not this is a 
source of the problem.


> Step 3, time 0.006 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.337002, max 0.559171 (between atoms 1 and 4)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>       1      2   90.0    0.1006   0.1091      0.1000
>       1      3   90.0    0.2058   0.1141      0.1000
>       1      4   90.0    0.3028   0.1559      0.1000
> Back Off! I just backed up step3b_n3.pdb to ./#step3b_n3.pdb.1#
> Back Off! I just backed up step3b_n4.pdb to ./#step3b_n4.pdb.1#
> Back Off! I just backed up step3c_n2.pdb to ./#step3c_n2.pdb.1#
> Back Off! I just backed up step3c_n3.pdb to ./#step3c_n3.pdb.1#
> Back Off! I just backed up step3c_n4.pdb to ./#step3c_n4.pdb.1#
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> Segmentation fault
> mkiytak at babil:~

LINCS warnings are the most common error reported to this list.  Please refer to 
the following pages for help:


If you still can't find your answer, refer to the list archive.  As I said, such 
errors are commonly reported.  Surely you'll find something useful.  The only 
thing that can be said right now is that your system is unstable.  Either you 
need better minimization or equilibration (or both), your .mdp settings are 
incorrect, or the free energy code is causing an instability (which is a symptom 
of the first two points, it does not suggest the free energy code is not working).



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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