[gmx-users] Segmentation fault (core dumped) during EM

Tushar Ranjan Moharana tusharranjanmoharana at gmail.com
Thu Apr 23 13:11:50 CEST 2015

Dear all,
I want to simulate lid opening of lipase in presence of triglyceride
micelle. I made micelle and equilibrate it in GROMACS (em, nvt, npt and md
) using CHARM36 force field. Dock triglyceride with lipase and put the
docked complex close to micelle. I changed the atomtype after docking to
match with CHARM36 atom type. I solvated the micelle lipase complex and
added required ions for charge neutrality. Then I proceeds to em there I am
getting the following error

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =         2000
Segmentation fault (core dumped)ot=         -nan Fmax= 1.31533e+09, atom=

I have shared some of my file which may be helpful in trouble shooting by
dropbox (everyone can asses). the links are as follow

tepa.itp is parameter file for triglyceride (triEPA)

topol.top is the system topology file

wt_gt_wp_tepa_micell_ion.gro is the structure file (just before em)

mdp file for energy minimization

calcium.itp and zinc.itp are distance restraint to protect the calcium and
zinc binding domain of my lipase

Any suggestion is most welcome.

Thanks for your time and effort.

Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB

"A society with free knowledge is better place to live than a society with
free food."

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