[gmx-users] how to prove the charges in rtp file!

Anton Feenstra feenstra at chem.vu.nl
Tue Apr 15 11:02:01 CEST 2003

nanyu101 wrote:
> Dear gmx-users,
>   I have done some simulation for a polyester and generated its rtp file myself.Some of partial charges in my residue were from a reference literature.Because I do it for a polyester, I should prove it firstly with ab initio results.I try to do it as follows:

Dear Xianhui,

The answer to your question is actually a whole area of reasearch:
force field development. Energies you get from MD or after energy
minimizations are generally *not* comparable to single point energies
from Quantum calculations, and the same goes for energy differences.
In MD/EM the energy is simply the sum of all pairwise interactions
as defined in the forcefield. In QM, the energy is actually a
physical property of the molecule.

For e.g. liquids (DMSO, water), the first things to optimize when
adjusting forcefield parameters, are density and heat of vaporization.
Internal parameters (bond lengths and angles), are usually taken from
crystal structures, or directly from QM calculations. For polymers,
I am not sure how best to do it, but you should be able to find some
literature about this... If your polymer will be solvated, be sure
also to get the solvation (free) energy of the monomers correct.

As for charges, in the Gromacs & Gromos forcefields, these are taken
more or less as adustable parameters. Usually they are about half of
the charge you would get from QM calculations, but it depends. Things
like density, hydrogen bond strength etc. depend on the charge.

If the minimized structure you get out of your EM is not what it
should be, check the angle and dihedral parameters first. But also
charges might have a (big) effect; sometimes you may have to exclude
internal charge-charge interactions (by adding an explicit [exclusions]
section to your .rtp or .top), or you may have to adjust the charges

Hope this gets you going for a bit!


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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