[gmx-users] Do I need to add hydrogens?
feenstra at chem.vu.nl
Fri Jan 23 10:59:07 CET 2004
Madhuri Agashe wrote:
> I had further questions:
> 1. why should we not use ffgmx2 forcefield?
It's very old, and the explicit hydrogens are not parametrized at all.
> 2.how is OPLS better than ffgmx2?
It's newer and it is a real all atom forcefield.
> 3.How should one go about using OPLS given the fact that gromacs first looks
> for the .rtp and .atp files in usr/local/share/gromacs/top?
Gromacs (or, pdb2gmx and grompp) first looks in the current directory, and
only then it looks in */gromacs/top. So, put any updated and/or modified
file in your current directory.
> 4.In octanol.itp that you had attached to the previous reply, Carbons are
> defined with no hydrogens wheras oxygen has a hydrogen defined too. Why is
> this so? Does this mean that hydrogens attached to carbons need not be
> 5. The gromacs library has decane.itp. This molecule has ONLY carbons
> defined and no hydrogens. Does this mean that while defining alkane/alkene
> chains, we do not need to define hydrogens?
> 6. When a Carbon is defined as a C2 carbon, does it assume 2 implicit
> hydrogens? Is this Carbon so parameterized so as to include the effect of
> these implicit hydrogens?
This is the principle of 'United atoms'. It should be described in the manual.
If that doesn't help, check the archives or any decent book on molecular modeling.
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