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

[S.M. Golam Mortuza]

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.
 
Regards,Golam Mortuza


      On Monday, June 29, 2015 11:01 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
   

 

On 6/29/15 1:56 PM, S.M. Golam Mortuza wrote:
> Hi Justin,
> Thank you so much for your suggestion. Also, thanks a lot for taking a close look at the paper. I've contacted with the authors of the paper and asked the topology. In the mean time, I've tried simulating a system of a benzene using the method described in the paper, and it ran successfully. So, I am assuming it's the problem with the value of polarization for carbon nanotube.
>

Good to hear!

> Anyway, I've compiled the new code as per your suggestion. I am just wondering whether it's possible to merge this new code with the previous version of gromacs, which is already installed in my computer. Or, are they two different executables and need to be run separately based on my preference? If the latter case, what is the executable names for the new code. For instance, we use grompp, mdrun, etc. for the regular version of gromacs. Are they similar for the new code as well?
> Please accept my apology if these are very dumb questions. Actually, I am not understanding which executables need to be used for the new code to run a simulation, since I do not see the common executables of gromacs (e.g., grompp, mdrun, etc.) after I installed the new code. Any help would be highly appreciated.

You can't merge the new code with old executables.  You simply have to install 
the new code and use it.  The new GROMACS convention is a single binary called 
"gmx" and everything else is called as a module of it.  So instead of "grompp" 
you now have "gmx grompp" and "mdrun" is "gmx mdrun," etc.  Functionally there 
is no difference, it's just a new syntax.

-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

==================================================