[gmx-users] gromacs bond type

David van der Spoel spoel at xray.bmc.uu.se
Sun Jul 13 09:14:18 CEST 2008

prasun kumar wrote:
> dear users,
> I am trying to get some information about the bond type,angle type and 
> dihedral angle type.
> can any one please tell me what is the bond type of C-F.angle type for 
> F-C-F,dihedral angle type of F-C-C-O &F-C-C-H.
> Or any one can tell me how to define the gromacs type for bonds,angles.I 
> tried to read the 5th chapter but not getting any thing.
> actually i am lookig forward to include TFE in the rtp file for my 
> simulation of peptide in TFE.
> Please help me.
> Thanx in advance

Try reading literature. There are a few recent publications about models 
for TFE. The GROMACS manual is a bit terse maybe, but all information 
about potentials is available in Chapter 4, ad Ch. 5 is up-to-date as 
well about topology format.

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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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