[gmx-users] Dihedral form

[Erik Marklund]

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-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Erik Marklund [erikm at 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
> erikm at 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
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html