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.
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
