[gmx-users] Fw: Simulation of polarizable Carbon nanotubes

[Justin Lemkul]

On 7/8/15 4:57 PM, S.M. Golam Mortuza wrote:
> Hi Justin,
> Thank you so much for your suggestion.
> Before, trying to simulate polarizable CNTs using the new code based on drude oscillator, I've been trying to simulate systems of SWM4-NDP water with KCl to make myself familiarize with the new code.
>
> At first, I was incorporating drude parameters (e.g. drude=yes with SCF, NPT), but, I was getting segmentation fault. Then, I turned off the drude parameters and ran the simulation. I did not get the error. However, the system is freezing (no movement of atoms). I am assuming it's an artifact, but, I'm not sure what is the reason behind this. I simulated the similar system using older version of gromacs (4.6.1), and I did not face the issue of artifacts. Can you please provide me any solution to overcome this issue? FYI: I've been using isotropic polarizability of water and ions.
>
> Thanks in advance. I modified the .mdp file that you provided in your recent paper on drude oscillator in Gromacs. My .itp file looks like:
> [ defaults ]
> LJ    Geometric
>
> [ atomtypes ]
> ;name        mass      charge   ptype   c6    c12
>     WO    15.99940       0.0     A       0.0    0.0
>     WH     1.00800       0.0     A    0.0    0.0
>     WS     0.0           0.0     S       0.0    0.0
>     WD      0.0        0.0    D       0.0    0.0
>     Kc   39.0983        0.0     A     0.0        0.0
>     Ks    0.0000000     0.0     S     0.0        0.0
>    CLc   35.45300       0.0     A     0.0        0.0
>    CLs    0.0000000     0.0     S     0.0        0.0
>
> [ nonbond_params ]
> WO      WO      1       3.67796770E-03   3.83182123E-06
> WO      Kc      1      2.46E-03   2.492E-06
> WO      CLc     1      6.69E-03   1.84E-05
> Kc      Kc      1      1.646E-03   1.62E-06
> CLc     CLc     1      12.16158E-03   8.8248256E-05
> Kc      CLc     1      4.474E-03   1.196E-05
>
> [ moleculetype ]
> ; molname    nrexcl
> SOL        2
>
> [ atoms ]
> ; id    at type    res nr     residu name    at name        cg nr    charge
> 1    WO    1    SOL        OW        1    1.71636
> 2    WH    1    SOL        HW        1    0.55733
> 3    WH    1    SOL        HW        1    0.55733
> 4    WD    1    SOL        DW        1     -1.11466
> 5    WS    1    SOL        SW        1    -1.71636
>
> #ifdef ANISOTROPIC
> [ water_polarization ]
> ; See notes above. Alphas in nm^3 (See ref. above)
> ; O H H D S funct  al_x     al_y      al_z           rOH    rHH    rOD
>    1 2 3 4 5 1    0.001415 0.001528 0.001468     0.09572    0.15139 0.0137408
>
> #else
>
> [ polarization ]
> ; See notes above.    alpha (nm^3)
> 1    5    1     0.00097822
> #endif
>
> [ bonds ]
> 1       2       1   0.09572     458148.
> 1       3       1   0.09572     458148.
>
> [ angles ]
> ; i     j       k
> 2       1       3    1   104.52     417.6
>
> [ dummies3 ]
> ; Dummy from            funct    a        b
> 4       1       2       3       2       0.5      0.024034
>
> [ exclusions ]
> ; iatom excluded from interaction with i
> 1    2    3    4    5
> 2    1    3    4    5
> 3    1    2    4    5
> 4    1    2    3    5
> 5    1    2    3    4
>
> [ moleculetype ]
> ; molname       nrexcl
> K+            1
> [ atoms ]
> ; id    at type res nr  residu name     at name cg nr   charge
> 1       Kc       1       K             Kc    1        2.580968
> 2       Ks       1       K             Ks    1       -1.580968
> [ polarization ]
> ; See notes above.      alpha (nm^3)
> 1       2       1       0.000830
> [ exclusions ]
> ; iatom excluded from interaction with i
> 1       2
> 2       1
>
> [ moleculetype ]
> ; molname       nrexcl
> Cl-             1
>
> [ atoms ]
> ; id    at type res nr  residu name     at name cg nr   charge
> 1       CLc     1       CL             CLc     1        2.457187
> 2       CLs     1       CL             CLs     1       -3.457187
>
> [ polarization ]
> ; See notes above.      alpha (nm^3)
> 1       2       1       0.0003969
>
> [ exclusions ]
> ; iatom excluded from interaction with i
> 1       2
> 2       1
>
>
> Let me know if you require any further information. I've taken all the parameters from literature on SWM4-NDP water and monovalent ions.
>

Please send me all of the required input files off-list, along with a list of 
your exact sequence of commands.  I'll have to run through a debugger to figure 
out where the seg fault is coming from.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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