[gmx-users] Coulomb energies
inmuno_cl at yahoo.com
Mon Mar 21 03:19:45 CET 2005
Thanks David for you replay. Actually te ligand BZA has a charge -1 so, Do you think that it is the problem? in this case How can I improve this?. In my simulations I used RF with epsilon=78 , FF gromos 96, Coulomb radio= 1.0 and Van der Wals radio= 1.0, to measure Van der Wals energies cut-off. I used nlist=5 y rlist= 10 too. The rest of the parameters are the standars, temperature coupling and pressure coupling = berendsen.
On Sat, 2005-03-19 at 09:49 -0800, Cesar Lopez wrote:
> Dear Gromacs users:
> I used Gromacs to repeat a simulation of the method
> LIE (Peter A. Kollman 1999 ) with the Trypsin and the
> I have obtained similar values of binding free energy,
> at least using LIE method and the clasical equation,
> when I analyzed the punctual energies of my sistem (
> drug in water and drug in protein) I saw that the LJ
> energier are very similar to the Wan der vals
> aproximation that they used, but when I compare the
> Coulomb energies (In Gromacs S-R Coulomb energies)
> are very different, for example ,They had 114 Kcal/mol
> in protein and 110 Kcal/mol in water, while I obtained
> 240 and 220 KJ/mol in each case.
Is this really the interaction energy? Or do you have a charged ligand?
The differences are very similar though, so somewhere there seems to be
a constant energy term. How about cut-off treatment, force field...
> My questions are:
> Can different methods obtain different coulomb
> Is there any difference If I use constraints????? or
> maybe cutt-offs?
> Is the forcefield the guilty?
> The strange Is that I have repeated with more proteins
> and the behavior is similar , differents coulomb
> energies, similar LJ to the experiments, and the free
> energy similar to the experimental.
> Thanks for your time
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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