[gmx-users] Regarding Coulomb-14 Energy

[Justin Lemkul]

On 4/18/18 5:49 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?
>
> ricin + urea (298K): 3.41E+04
> ricin + urea (350K): 3.41E+04
> ricin + urea (450K): 3.40E+04

Different systems, different topologies = different results.

This quantity on its own has no physical meaning.

-Justin

> 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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-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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