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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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