Hi Mark. Haven't got exactly what you said. So let me rephrase myself:
The CF4 molecule doesn't have dihedrals nor intramolecular LJ and coulombic contributions. What kind of contribution am I missing that makes potential energy minus bond stretching minus angle bending *different* from Lj + coulomb(SR) + coulomb (LR) + Disp correction? Thanks a lot in advance, Sincerally yours, Jones On 6/23/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
> The intermolecular energy in the liquid should no be equal to the sum of > the > LJ, coulomb(SR, coulb(LR) and Disp Correction? And, that correct, > shouldn't > it be equal also to the potential energy minus bond minus angle bending > energies? What am I missing, that is making me have both different? Dunno since we can't read your mind about the sort of calculation you did... What does your logfile have? > Another question: what exactly is the "coul. recip." standing for? I > expected it had to be included in the above sums also, but the high values > it yelds would be nonsense. It's the reciprocal space sum of the Ewald method you're using. It sounds like you should read the section in chapter 4(?) of the manual that describes this. The reason it's large is that it has (roughly) all the long-range contributions from all of the atoms, and I don't think these can be sensibly broken down into by-atom components. So if you're interested in determining intermolecular energies, for some reason, you should design a simulation protocol that has a chance of doing this. In a GROMACS context, that probably means GRF electrostatics. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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