[gmx-users] Simulation of polarizable Carbon nanotubes

[S.M. Golam Mortuza]

Dear Gromacs Users,
I am trying to run a simulation using polarizable force field for carbon nanotube (CNT), which has 304 carbon atoms. As a test purpose, I am trying to simulate a system containing a pair of KCl ion in an infinite carbon nanotube. However, my ultimately goal is to simulate a system comprising water, KCl inside the CNT. 

I have been trying to mimic the paper http://www.sciencedirect.com/science/article/pii/S0927025607000456
Also, I have been following the thread on this topic:
https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg10520.html
 Again, as a test purpose, I have put only one dummy atom (atom id 306), which is harmonically connected with a shell atom (atom id 305), inside a hexagonal ring (atom id: 1 20 38 39 57 58). I have used position restrain for the nanotube and the dummy atom. I think I've followed every procedure that Justin and Peter suggested in the thread.  Some parts of my itp file of the CNT looks like:

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
1    CJ    1    CNT    C    1    0.25    12.011    ;    qtot    02    CJ    1    CNT    C    2    0    12.011    ;    qtot    0
3    CJ    1    CNT    C    3    0    12.011    ;    qtot    0..........................................................................................................................................................................
305    SL    1    CNT    SL    1    -1.5    1    ;    qtot    0 ; Shell
306    VS    1    CNT    VS    300    0    0    ;    qtot    0 ; Dummy
[ polarization ]
; virtual_site    shell    functiontype    alpha (in nm^3)
    306        305    1        0.1296


[bonds]........
[angles]......
[dihedrals]......
[ virtual_sitesn ]
; Site funct from 
306 1 1 20 38 39 57 58

[ exclusions ]
; iatom excluded from interaction with i
305 1    2    3    4    5    6    7    8    9  ..... 304   ; I have used exclusions from the shell atom with all carbon atoms of the nanotube. I am not sure whether I should exclude more exclusions. 

Sometimes, the simulation gives error as:EM did not converge in 20 iterationsSegmentation fault (core dumped)
I tried to play with different parameters, such as polarizablity, exclusion list, etc. However, sometimes, I can see following messages in my window, and the simulation does not move further.

starting mdrun 'KCl electrolyte in CNT'
100000 steps,    100.0 ps.
MDStep=    0/ 0 EPot: -4.83364532e+02, rmsF: 2.17e+01

step 0MDStep=    1/ 0 EPot: -4.34285614e+02, rmsF: 2.19e+01
MDStep=    2/ 0 EPot: -3.03536743e+02, rmsF: 2.22e+01
MDStep=    3/ 0 EPot: -1.36375397e+02, rmsF: 2.24e+01
MDStep=    4/ 0 EPot: 1.27241879e+01, rmsF: 2.25e+01

NOTE: Turning on dynamic load balancing

MDStep=    5/ 0 EPot: 1.01205765e+02, rmsF: 2.27e+01
MDStep=    6/ 0 EPot: 1.15893883e+02, rmsF: 2.28e+01
MDStep=    7/ 0 EPot: 7.45831146e+01, rmsF: 2.28e+01
MDStep=    8/ 0 EPot: 1.53622913e+01, rmsF: 2.29e+01
MDStep=    9/ 0 EPot: -2.12497330e+01, rmsF: 2.29e+01
MDStep=   10/ 0 EPot: -1.05190954e+01, rmsF: 2.29e+01
MDStep=   11/ 0 EPot: 4.68694420e+01, rmsF: 2.29e+01
MDStep=   12/ 0 EPot: 1.29762100e+02, rmsF: 2.29e+01
MDStep=   13/ 0 EPot: 2.02292053e+02, rmsF: 2.29e+01
MDStep=   14/ 0 EPot: 2.34559998e+02, rmsF: 2.29e+01
MDStep=   15/ 0 EPot: 2.15615555e+02, rmsF: 2.29e+01
MDStep=   16/ 0 EPot: 1.57610504e+02, rmsF: 2.30e+01
MDStep=   17/ 0 EPot: 8.87061996e+01, rmsF: 2.30e+01
MDStep=   18/ 0 EPot: 4.16818733e+01, rmsF: 2.30e+01
MDStep=   19/ 0 EPot: 3.34845123e+01, rmsF: 2.31e+01
MDStep=   20/ 0 EPot: 6.07384720e+01, rmsF: 2.31e+01
MDStep=   21/ 0 EPot:          inf, rmsF: 2.30e+01

I have checked that my shell and dummy atoms remain close to each other. However, sometimes the CNT blows up. I would really appreciate if anyone can help me with this.
Justin,I have seen that your paper on polarizable force field has been published already. I am using gromacs version 4.6.1. Can I use the codes for polarizable force field in this version. Any sort of help would be highly appreciated.
Please let me know, if you need any further information. Thanks in advance.
 Regards,Golam Mortuza