[gmx-users] infinite molecule problems
feenstra at chem.vu.nl
Thu Oct 2 09:20:03 CEST 2003
Sherwin J. Singer wrote:
> 3) Is my procedure for making the topology file correct?
I'll just give some hints/idea's on this point...
> 3) Perhaps my procedure for making the topology file is wrong.
> The [ bonds ] and [ angles ] list seemed straightforward. To generate
> the [ pairs ] and [ dihedrals ] lists I listed all unique 1-2-3-4 walks
> through the crystal and listed each one under [ dihedrals ]. Then I
Generally you only need 'proper dihedrals' for rotatable groups, and
'impropers' for tetrahedral groups with united atoms (e.g. Ca in amino
acids) and for planar groups. I'd say for silicate you only need dihedrals
for the hydroxyls.
> took the 1-4 members of each of those walks and listed them under [
> pairs ], and I'm using the parameters for those 1-4 interactions from
> the ffgmx files. I was a little unsure about this last step, because in
> the discussion of the [ dihedrals ] section of the urea example (page
> 103 of the 3.1.1 Gromacs manual), it says to "do not forget to erase
> the 1-4 interactions in [ pairs ]!!" What does this mean?
Adding only a dihedral potential to the regular LJ and Coul interaction
between the 1-4 atoms in a dihedral doesn't reprocude the right behaviour
(i.e., not the right overall potential). The fix is to use 'special' or
'different' LJ parameters for these, and this is what is called 'pairs'
in Gromacs. So it means the normal LJ is erased and replaced by LJ 1-4
Generally, a 'pair' is needed for each rotatable group (i.e. for each
proper dihedral. For the silicate, again that would be only the hydroxyls.
> Also, I assigned charges to all the SI, OS, OA and HO atoms of my chunk
> of silicate. I could not find default charge parameters in the force
How did you determine your charges? Are they of the same order as the
charges found in the forcefield you use? (This can differ considerably
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