[gmx-users] segmentation fault during equilibration

niaz poorgholami poorgholami at gmail.com
Tue May 1 13:19:51 CEST 2012

Dear gmx users,
I am simulating a system including carbon nanotube(a finite
one)+water+surfactant and so far I have done these things:
1.I generated the topology of CNT ( opls force field) by this command:
g_x2top -f cnt.pdf -o cnt.top -nopairs -nexcl 3 -name CNT
2.I used TopolGen to produce topology of surfactant and I calculated
the charges of atomes by the RESP method and checked the
atomtypes to make sure that they make sence as well.so I changed some
atomtypes according to the opls.
3.I build a topol.top file that contains topolgy of CNT+surfactant.
4.I created the initial configuration for the CNT+surfactant by means
of packmol.
5.I used editconf and genbox with these command:
editconf -f CNTSUR.pdb -o newbox.gro -d 0.7 -bt cubic
genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
6.I run grompp and genion for adding the ions:
grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
genion -s ions.tpr -p topol.top -o solv_ions.gro -nname BR -nn 28
7.I run grompp again for energy minimization:
grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tpr
mdrun -deffnm em
the em_real.mdp file contains:
; Parameters describing what to do, when to stop and what to save
integrator	= steep		; Algorithm (steep = steepest descent minimization)
emtol		= 1000.0  	; Stop minimization when the maximum force < 10.0 kJ/mol
emstep          = 0.01          ; Energy step size
nsteps		= 70000	        ; Maximum number of (minimization) steps to perform
energygrps	= UNK LIG	; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
nstlist		= 1		    ; Frequency to update the neighbor list and long range forces
ns_type		= grid		; Method to determine neighbor list (simple, grid)
rlist		= 0.9		; Cut-off for making neighbor list (short range forces)
coulombtype	= PME		; Treatment of long range electrostatic interactions
rcoulomb	= 0.9		; long range electrostatic cut-off
rvdw		= 1.4 		; Periodic Boundary Conditions (yes/no)
pbc		= xyz 		; Periodic Boundary Conditions (yes/no)

8.then I made an index file for CNT and surfactant and used genrestr
to restraint the CNT and surfactant during equilibration.
9.I run grompp and mdrun with these command:grompp -f nvt.mdp -c
em.gro -p topol.top -o nvt.tpr -n index.ndx
                                            mdrun -deffnm nvt
and after passing 42900 of 50000 steps, segmentation fault occured.I
checked the log file but it did not contain any errors and I also used
VMD to see trajetory but I did not see anything wrong.
I would be pleased if anyone could help me how to fix this.

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