[gmx-users] gromacs.org_gmx-users Digest, Vol 168, Issue 45
Justin Lemkul
jalemkul at vt.edu
Thu Apr 12 19:12:54 CEST 2018
On 4/12/18 2:55 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.
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
>
>
> [ bonds ]
> 1 2 2 0.1340 1.0500e+07
> 1 5 2 0.1340 1.0500e+07
> 1 8 2 0.1340 1.0500e+07
> 2 3 2 0.1000 1.8700e+07
> 2 4 2 0.1000 1.8700e+07
> 5 6 2 0.1000 1.8700e+07
> 5 7 2 0.1000 1.8700e+07
> 8 9 2 0.1000 1.8700e+07
> 8 10 2 0.1000 1.8700e+07
>
>
> [ angles ]
> 1 2 3 2 120.00 390.00
> 1 2 4 2 120.00 390.00
> 1 5 6 2 120.00 390.00
> 1 5 7 2 120.00 390.00
> 1 8 9 2 120.00 390.00
> 1 8 10 2 120.00 390.00
> 3 2 4 2 120.00 445.00
> 6 5 7 2 120.00 445.00
> 9 8 10 2 120.00 445.00
> 2 1 5 2 120.00 670.00
> 5 1 8 2 120.00 670.00
> 8 1 2 2 120.00 670.00
>
>
> [ pairs ]
> ; ai aj funct c0 c1
> 2 6 1 0.000000e+00 0.000000e+00
> 2 7 1 0.000000e+00 0.000000e+00
> 2 9 1 0.000000e+00 0.000000e+00
> 2 10 1 0.000000e+00 0.000000e+00
> 5 3 1 0.000000e+00 0.000000e+00
> 5 4 1 0.000000e+00 0.000000e+00
> 5 9 1 0.000000e+00 0.000000e+00
> 5 10 1 0.000000e+00 0.000000e+00
> 8 3 1 0.000000e+00 0.000000e+00
> 8 4 1 0.000000e+00 0.000000e+00
> 8 6 1 0.000000e+00 0.000000e+00
> 8 7 1 0.000000e+00 0.000000e+00
>
> [ dihedrals ]
> ; ai aj ak al gromos type
> 2 1 5 6 1 180.000 33.5 2
> 2 1 5 7 1 180.000 33.5 2
> 2 1 8 9 1 180.000 33.5 2
> 2 1 8 10 1 180.000 33.5 2
> 5 1 2 3 1 180.000 33.5 2
> 5 1 2 4 1 180.000 33.5 2
> 5 1 8 9 1 180.000 33.5 2
> 5 1 8 10 1 180.000 33.5 2
> 8 1 2 3 1 180.000 33.5 2
> 8 1 2 4 1 180.000 33.5 2
>
> Thank you
>
> Regards
> Zaved Hazarika
> PhD Scholar
> Dept.of Molecular Biology and Biotechnology
> Tezpur University
> India
>
>> 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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