Hello again. It's pretty clear now for me thanks. I still have a little problem due to the unphysical trend of the BKS potentials for r --> 0 : it goes to minus infinity. The atoms can thus collide in case of a high temperature (providing them enough velocity to overcome the barrier) and I get the following error which I suppose is connected to this problem :
"Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 8 ]" Practically, at ambient temperatures of the order of 300 K, it doesn't happen but I want to anneal first at 5000 K to get a melt SiO2 and then quench it to 300 K. The standard procedure to avoid particle colliding is to add a hard repulsive part acting only on short distances. Is it possible to add a repulsive part on short distances only (something like Vrep(r)=a*(r-r0)^4 with r0 being the distance at which the barrier is at its maximum) and how could I do it ? The potential energy should then be V=Vrep(r) for r < r0 and V=V_BKS(r) for r > r0. If it's not possible analytically, I assume I should use a user specified potential function by making a table.xvg file with the x, f(x), f'(x), etc ... as it is mentioned in the manual (p133 and p148) ? David Waroquiers - PhD Student Université Catholique de Louvain Laboratoire de Physico-Chimie et de Physique des Matériaux European Theoretical Spectroscopy Facility Mark Abraham wrote: > David Waroquiers wrote: > > Hello > > > > I'm trying to simulate amorphous SiO2 with the use of the BKS potentials > > (van Beest, B. W. H.; Kramer, G. J. & van Santen, R. A. - Phys. Rev. > > Lett., American Physical Society, 1990, 64, 1955-1958). > > > > According to these potentials, I should use the Buckingham potentials > > with user-defined parameters plus a coulomb part with user-defined > > charges for each atom type. I don't need any other forcefield from > > GROMACS. > > > > When I try to preprocess my topology file and get the .tpr binary file > > in order to start the simulation, I get the following message in the > > terminal : > > > > processing topology... > > Generated 0 of the 3 non-bonded parameter combinations > > Excluding 0 bonded neighbours molecule type 'O' > > Excluding 0 bonded neighbours molecule type 'Si' > > > > I don't understand why my non-bonded parameters aren't generated ... > > "Generation" refers to the process described in (probably) chapter 4 of > the manual where all possible pairwise interactions between a set of > atom types are calculated from generic parameters characteristic of the > two atom types involved (see your [atomtypes] entries). An alternative > is to describe the pairwise interactions specifically, as you have done. > Thus GROMACS didn't need to generate any, and reports this fact. > > 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
