[gmx-users] pairs potential
lastexile7gr at yahoo.de
Wed Jul 9 12:01:10 CEST 2008
I would like to know the potential that the atoms under the pairs section are using. For that reason, I tried to test the most simple of systems, that is a two hydrogen system atom model.
The sigma in my pairs section is 0.23160nm, yet I do not observe the pairs potential to be zero in that value. My table extension is 5nm and my box size 50nm in any side.
The potential becomes zero for the second time, when the distance becomes equal to the value of the table extension parameter. Now, if the pairs are using lennard jones potential, I think that the first zero point (of the LJ-14 output) should be at a distance equal to the sigma value under the pairs section. I get zero neither there nor in the sigma of the nonbond_params nor in rvdw-switch values.
I do not think that the pairs potential is a shifted one either because I get a wave like function till the potential becomes zero at the table extension value. Could you shed some light on this, because up to now in this section gromacs is a black box to me.
PS:Sorry for any double posting due to network problems
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