[gmx-users] prodrg

[David van der Spoel]

On Mon, 2004-10-04 at 15:21, Hector Martinez-Seara Monne wrote:
> David van der Spoel wrote: 
> > On Mon, 2004-10-04 at 08:13, Hector Mrz-Seara Monne wrote:
> >   
> > > Thank you David for your help, I'm quite new in gromacs and many things 
> > > still lack on
> > > my knowledge. Well I'm trying to reduce all the constants forces in the 
> > > *.itp file of my monomer.
> > > By the way, the only constants that worry you where those of the 
> > > improper dihedral or also of the proper once
> > > with the asterisk. And why PRODRG  duplicate the colums of definitions
> > > 
> > > (c0    c1 m)  (c0   c1 m)
> > > 
> > > , this is normal(this confuses me since the beginning)?
> > >     
> > This has to do with free energy calculations where you go from one
> > definition to another. Does prodrg produce the m for impropers as well?
> > 
> >   
> 
> Hi david,
> 
> All contants forces definition provide from PRODRG, the number 1673 is
> the given by the program
> but for your coments is quite hight. Sorry, but for your answer I
> can't know if you think I have also problems
> with the proper dihedral also, Can you clarify this point please. 
> 
Could be. Compare to similar dihedrals in the force field (e.g.
ffgmxbon.itp)
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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