Hi,
15 nov 2012 kl. 15.41 skrev Laura Leay:
> Thanks Eric,
>
> Just to clarify (I hope this notation is in fact clear):
>
> E=0.5k [ 1 - cos( n*phi - n*phi_o +180 ) ] = 0.5k [ 1 + cos(n*phi - n*phi_o)]
> ^ this whole equation is Dreiding ^this whole equation is
> Dreiding converted to the form in Gromacs
>
> This would mean that:
> 0.5k in Dreiding = k in Gromacs
> n in Dreiding = n in Gromacs
> n*phi_o +180 in Dreiding (original form) is phi_s in the Gromacs notation
> from the original post
>
I think that's correct.
>
> I hope this makes sense!
>
> Laura
>
>
> ________________________________________
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
> of Erik Marklund [er...@xray.bmc.uu.se]
> Sent: 15 November 2012 13:37
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Dihedral form
>
> You could shift the reference angle by pi, which changes the sign of the
> cosine.
>
> Best,
>
> Erik
>
> 15 nov 2012 kl. 14.25 skrev Laura Leay:
>
>> All,
>>
>> I would like to parameterise the Dreiding force field for use with Gromacs.
>> One thing I am not sure about is how to parameterise the dihedrals
>>
>> The Dreiding paper has the form;
>>
>> E= 0.5k { 1 - cos[ n( phi - phi_o)]}
>>
>> However I cannot find this form in the Gromacs manual. The closest I can
>> find in the Gromacs manual is:
>>
>> E = k [ 1 + cos(n*phi - phi_s) ]
>>
>>
>> Does anyone know of a way to use the Dreiding form in Gromacs, or to convert
>> to a form that is more suitable for use with Gromacs?
>>
>> Many thanks,
>> Laura
>> --
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>
> -----------------------------------------------
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: +46 18 471 6688 fax: +46 18 511 755
> er...@xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
>
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 6688 fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html
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