[gmx-users] Regarding Coulomb-14 Energy

[Mark Abraham]

Hi,

On Wed, Apr 18, 2018 at 10:50 AM <zaved at tezu.ernet.in> wrote:

> >> Dear Mark
> >> Thank you for the kind response.
> >> H with +0.418 charge and N with -0.845 charge is contributing towards
> coulomb 14 interaction. So what is the amount of interaction between
> one
> >> single H and N (3 bonds apart)? Kindly correct me if I am wrong.
>
> Thank you Justin for your kind response.
>
> I have also simulated ricin in presence of urea(1843 urea) with gromos54a7
> ff. However with urea having similar kind of topology to that of Gdm, I am
> getting the Coulomb 14 with positive values. Why in this case the C14 is
> not having negative value?
>

Same as I said last time. It's a subtotal from a lot of components. Its
value reflects those values. Why would you care whether it is positive or
negative? There's no reason to expect such a subtotal to correlate with
anything useful or physical.

Mark


> ricin + urea (298K): 3.41E+04
> ricin + urea (350K): 3.41E+04
> ricin + urea (450K): 3.40E+04
>
> Urea Topology:
>
> [ UREA ]
>  [ atoms ]
>    OU OUREA    -0.39000     0
>    CU CUREA     0.14200     0
>   N1U NUREA    -0.54200     0
>  H11U     H     0.33300     0
>  H12U     H     0.33300     0
>   N2U NUREA    -0.54200     0
>  H21U     H     0.33300     0
>  H22U     H     0.33300     0
>  [ bonds ]
>    OU    CU    gb_44
>    CU   N1U    gb_45
>    CU   N2U    gb_45
>   N1U  H11U    gb_2
>   N1U  H12U    gb_2
>   N2U  H21U    gb_2
>   N2U  H22U    gb_2
>
> Thank You
>
> Regards
> Zaved
>
> > Simply calculate it with Coulomb's Law and apply the 1-4 electrostatic
> scaling factor (if your force field uses one).
> > -Justin
> >> Here is my Gdm topology
> >> [ moleculetype ]
> >> ; name  nrexcl
> >> GDM         3
> >> [ atoms ]
> >> ;   nr    type   resnr  residu    atom    cgnr  charge       MASS
> >>       1      C        1    GND       C1       1       1.027  13.019
> >>       2     NT        1    GND       N2       2       -0.845 14.0067 3
>
> H        1    GND       H3       2       0.418  1.008
> >>       4      H        1    GND       H4       2       0.418  1.008
> >>       5     NT        1    GND       N5       3       -0.845 14.0067 6
>
> H        1    GND       H6       3   0.418      1.008
> >>       7      H        1    GND       H7       3       0.418  1.008
> >>       8     NT        1    GND       N8       4       -0.845 14.0067 9
>
> H        1    GND       H9       4       0.418  1.008
> >>       10     H        1    GND       H10      4       0.418  1.008
>
> >>> Hi,
> >>> Presumably Gdm has atoms connected by three adjacent bonds that
> generally
> >>> have negative potential, and there's enough Gdm to make the total for
> the
> >>> system negative. It's generally a good idea to understand how the
> topology
> >>> you're using for Gdm works.
> >>> Mark
> >>> On Tue, Apr 10, 2018 at 2:23 PM <zaved at tezu.ernet.in> wrote:
> >>>> Dear Gromacs Users
> >>>> I have simulated ricin in presence of GdmCl (1519 Gdm and 1519 Cl)
> with
> >>>> gromos54a7 ff. Simulations have been performed for 100ns each at
> 298K,
> >>>> 350K and 450K.
> >>>> The Average Coulomb-14 Energies are as follows:
> >>>> ricin in water (298K) : 3.42E+04 (positive value)
> >>>> ricin in water (350K) : 3.41E+04 (positive value)
> >>>> ricin in water (450K) : 3.40E+04 (positive value)
> >>>> ricin + GdmCl  (298K)  :-3.16E+06 (negative value)
> >>>> ricin + GdmCl  (350K) : -3.17E+06 (negative value)
> >>>> ricin + GdmCl  (450K) : -3.17E+06 (negative value)
> >>>> Can anyone suggest me why there is a (10 to the power 10) fold
> difference
> >>>> of average Coulomb-14 energy of ricin in presence of water and ricin
> in
> >>>> presence of GdmCl?
> >>>> Thank You
> >>>> Regards
> >>>> Zaved
>
>