David van der Spoel
spoel at xray.bmc.uu.se
Mon Oct 4 16:12:55 CEST 2004
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.
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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