[gmx-users] gromacs.org_gmx-users Digest, Vol 168, Issue 45

[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.

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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