[gmx-users] energy terms during minimization
David van der Spoel
spoel at xray.bmc.uu.se
Thu Nov 21 09:10:29 CET 2002
On Wed, 2002-11-20 at 16:55, Ester Chiessi wrote:
> Hi all,
> During the energy minimization of my system ( an oligomer of poly(vinyl
> alcohol)) in a water box, I noted some anomalies:
> with sd and emtol 1000, the energy contributions 'bond', 'angle', 'dihe',
> 'LJ(1-4)', 'Coulomb(1-4)' increase while LJ(SR) and Coulomb(SR) decrease
> and govern the trend of the potential energy
> ('bond' increases from the step 0 of about 5000 kJ/mol, 'angle' of about
> 3000, LJ(SR) decreases of about 10000 and Coulomb(SR) decreases of about
This is completely normal, potential energy is minimized. You could in
principle have an error in the topology as well, but if energies start
out normal this usually isn't the case. At room temperature bonds and
angles each contributy by 1.25 kJ/mol to the energy (1/2 kT), this is a
> If I reduce the box size, the energy increases are smaller and seem
> proportional with the box size.
> If I perform the minimization in vacuo ( with no pbc) energy trends are
> more 'regular' (with a small increase of dihe and Coulomb(1-4)).
> When, in vacuo, I stress the convergence criterium to 100, the energy
> contributions show maxima and minima.
> Perhaps it's important to note that the oligomer starting structure is
> already very near to a 'minimum' structure.
> My question is:
> Should I have to consider these results a 'warning' for the correct
> simulation of the system?
> Or, if the final geometry is correct, can I go on with the dynamics?
> P.S. I tryed, as control, the minimization of the pure water box. I was
> surprised the LJ and Coulomb were always 0. Why?
That is incorrect.
> Thanks for any help
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 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
More information about the gromacs.org_gmx-users