[gmx-users] Reading Force field
Justin Lemkul
jalemkul at vt.edu
Mon Jul 18 16:20:31 CEST 2016
On 7/18/16 10:16 AM, Ben Tam wrote:
> 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 = ...... ?
>
These are computed during the MD, but without modifying the code there is no way
to print these out. You can of course apply Mark's approach by re-running
individual frames with different settings for energygrps to see how the energy
changes as a function of the coordinates.
-Justin
>
> 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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--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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