[gmx-users] Reading Force field

[Ben Tam]

Hi Mark,


Are there no way just to see the overall individual Lennard Jones interaction pairing through gromacs commands i.e. Mg - O = ...... Mg - C = ...... ?


Ben


________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abraham at gmail.com>
Sent: 18 July 2016 14:46
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Reading Force field

Hi,

For getting a feel for the sizes of things, you can make a system with two
atoms placed however far apart interests how, make a .tpr and then use
mdrun -rerun passing a file with one or more configurations where you want
to find out energy or force.

Mark

On Mon, Jul 18, 2016 at 3:35 PM Ben Tam <btam125 at hotmail.co.uk> wrote:

> Dear Gromacs User,
>
>
> I am trying to do a bit of debugging on the force field, how can I read
> the individual interaction between non-bonded potential? If it is not
> possible, can anyone tell me this is around the correct range for the
> lennard jones potential?  I am trying to debugging because when I am doing
> classical binding energy calculation, it gives me -4000 kJ/mol force (which
> is very unrealistic).
>
>
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 2 yes 0.5 0.833
>
> [ atomtypes ]
> ; name      at.num  mass     charge ptype  sigma      epsilon
> Mg   12     24.3050    1.567       A       0.2691      0.464395
> C1    6     12.0107    0.937       A   3.39967e-01  3.59824e-01  ;AMBER
> C2    6     12.0107   -0.326       A   3.39967e-01  3.59824e-01  ;AMBER
> C3    6     12.0107    0.458       A   3.39967e-01  3.59824e-01  ;AMBER
> C4    6     12.0107   -0.235       A   3.39967e-01  3.59824e-01  ;AMBER
> O1    8     15.9994   -0.914       A   2.95992e-01  8.78640e-01  ;AMBER
> O2    8     15.9994   -0.767       A   2.95992e-01  8.78640e-01  ;AMBER
> O3    8     15.9994   -0.907       A   2.95992e-01  8.78640e-01  ;AMBER
> H4    1     1.00794    0.191       A   2.59964e-01  6.27600e-02  ;AMBER
> ;
> C5    6     12.0107    0.795       A   3.39967e-01  3.59824e-01  ;AMBER
> C6    6     12.0107   -0.090       A   3.39967e-01  3.59824e-01  ;AMBER
> C7    6     12.0107   -0.164       A   3.39967e-01  3.59824e-01  ;AMBER
> C8    6     12.0107    0.119       A   3.39967e-01  3.59824e-01  ;AMBER
> C9    6     12.0107    0.005       A   3.39967e-01  3.59824e-01  ;AMBER
> C10   6     12.0107   -0.032       A   3.39967e-01  3.59824e-01  ;AMBER
> C11   6     12.0107   -0.174       A   3.39967e-01  3.59824e-01  ;AMBER
> C12   6     12.0107   -0.269       A   3.39967e-01  3.59824e-01  ;AMBER
> C13   6     12.0107    0.632       A   3.39967e-01  3.59824e-01  ;AMBER
> O4    8     15.9994   -0.607       A   2.95992e-01  8.78640e-01  ;AMBER
> O5    8     15.9994   -0.517       A   2.95992e-01  8.78640e-01  ;AMBER
> HO    1     1.00794    0.340       A       0.0000      0.000000  ;AMBER
> H7    1     1.00794    0.131       A   2.59964e-01  6.27600e-02  ;AMBER
> H12   1     1.00794    0.106       A   2.64953e-01  6.56888e-02  ;AMBER
> F     9     18.9984   -0.203       A   3.11815e-01  2.55224e-01  ;AMBER
> HW    1     1.00794    0.417       A   3.06647e-01  8.80314e-01
> OW    1     15.9994   -0.834       A   3.15061e-01  6.36386e-01
>
> Thank you very much.
>
> Best regards,
>
> Ben
>
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