[gmx-users] Regarding Coulomb-14 Energy

[zaved at tezu.ernet.in]

>> 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?

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





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