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

nanyu101 nanyu101 at sina.com
Thu Apr 10 03:21:01 CEST 2003

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:
1. I try to do it from one, two, three, four,.............and twelve oligomer, I hope the relative energy of these oligomers is close to the results of ab initio.But I found some strange things.First, if I do energy minimization in Gromacs,I found the conformation was changed,so the energy was not right.I can't calculate the single point energy in Gromacs because the results seem a large deviation in the first step.
2.Energy time I try to run energy minimization, I found that the carbonyl oxygen and carbonyl carbon were optimized all the time and other parts of the molecule didn't change their conformations.So,I check the partail charges in carbonyl oxygen and carbon,carbonyl oxygen is -0.380  and carbonyl carbon is 0.58.It seems a bit large,but how can I change this partial charge correctly?
3.Energytime I add a residue to my oligomer,I think the changed energy is the same,but I found when I add a residue to 5-peptide,the energe changed 1kcal/mol larger than other time.I wonder what caused this change?
My force field is ffG43a2 in Gromacs!!! Can I do a simulation in ffgmx force field for a polyester?
Thanks for your any comments.

Best wishes,
Xianhui Wu  


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