[gmx-users] Questions concerning Gromacs

Thomas Koller koller-thomas at gmx.de
Wed Jan 5 08:14:17 CET 2011


I have some questions concerning the implementation in Gromacs:

1) I want to model a rigid anion of an IL (fixed bonds and angles). The cation is flexible. How can I do that without using constraint types? With LINCS or SHAKE, I can only fix, for instance, bonds with H atoms or all atoms. Can I use high values for the force constants?

2) When implementing improper dihedrals, I write the sequences of the four atoms in the [dihedraltypes] and then fix them in the [dihedral] directive. But I always get the error that the impropers are not defined in the default. What is my problem? I use function type 2. The sequence of impropers is: center atom - neighbor atom - neighbor atom- neighbor atom,
as I saw in the manual.

3) For function type 1 of the dihedrals, I implement the equilibrium angle, the force constant and the multiplicity (one value for all kinds). What should I do if I have, for instance, three equilibrium angles, different for the multiplicities (n=1,2,3). How can I implement that in the top file?

Thanks for your efforts!
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