[gmx-users] Re: amber parameters in gromacs

[Alan]

Hi Rolf,

On Thu, Jul 1, 2010 at 10:23, <gmx-users-request at gromacs.org> wrote:

> I used the GROMOS FF but changed the parameters (sigma, epsilon, charges,
> 1-4 interaction, combination rule for LJ, bond length strength, dihedrals,
> angles) so that they are equal to the parameters used by the other authors
> with their AMBER FF. The equations uses to calculate the energy are the
> same, that is why I expected to get the same results. ...so I guess this
> assumption is not true. Why is it not possible to use these parameters?
>

I understand that you're trying to simulate *only* glycerol and nothing
else. In principle your idea does hold water, but in the end it's full of
holes. GROMOS FF is conceived as an united-atom ff even if you have all
protons explicit. The biggest difference among others I see is the way how
dihedrals will be calculated. BTW, where's the reference to the article you
mentioned?

Do you want to rule out these potentials problems? Re-read the first email I
sent and do check the links I provided. From there you can start to know how
to use ffamber or, if you have your parameters in amber format (do you know
how to use tleap from AmberTools to generate a prmtop and inpcrd files?), to
use acpype (or amb2gmx) to convert them to gromacs format straightaway.


> Is there a way to get a topology of glycerol working with gromacs instead
> of writing it oneself? I've already tried the Prodrg Server but I didn't get
> proper results with this topology, either.
>

The basic answer is "yes" and my attempt to to answer that is above.

Cheers,

Alan

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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