[gmx-users] segmentation fault during equilibration

Justin A. Lemkul jalemkul at vt.edu
Tue May 1 14:42:26 CEST 2012

On 5/1/12 7:19 AM, niaz poorgholami wrote:
> 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

Unrelated to the crash, but if your longest cutoff is 1.4 nm, setting a 
solute-box distance of 0.7 nm will lead to trouble if you ever use NPT.  With 
just a small fluctuation in box dimension, you can easily violate the minimum 
image convention.

> 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)

What was the outcome of EM?  What were your values for Fmax and Epot?

> 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.

We need to see your complete .mdp file for the NVT run.  As of now, there is no 
indication of what is wrong.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list