[gmx-users]Re: pairs potential

Claus Valka lastexile7gr at yahoo.de
Mon Jul 21 12:11:05 CEST 2008

Hello,the pairs potential is a (classic) lennard jones potential till the value of table extension. The problem in my example was in the precision of the value of sigma. Under the pairs section I was able to put the value 0.23160, yet I could not in the gro file for the coordinates of the atoms, where there I could put only 0.231 or 0.232. Changing sigma to 0.231 I notticed that I get zero exactly at that distance. 
What I have noticed also is that table extension should be bigger than any pair distance in one's system. If it is so, and someone get errors, for example system exploding, probably there is a problem in one's topology.
Nikos--- Claus Valka <lastexile7gr at yahoo.de> schrieb am Mi, 9.7.2008:
Von: Claus Valka <lastexile7gr at yahoo.de>
Betreff: [gmx-users] pairs potential
An: gmx-users at gromacs.org
Datum: Mittwoch, 9. Juli 2008, 12:01


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.

Thank you,

PS:Sorry for any double posting due to network problems

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