[gmx-users] when using RB dihedral function, how to exclude 1-4 vdw ?

XunJie Yang yangxunj at mail.ustc.edu.cn
Fri Nov 20 09:45:44 CET 2009

Hello GMX users:
  I'm new to GMX and I'm now facing a problem. For short, it is about how to properly use the RB function.
  I'm now doing simulation with AMBER force field(ported to GMX by FFAmber), which employs Ryckaert-Bellemans function for dihedral, it is how FFAmber forcefield treats dihedral angles as the parameters provided are only for RB function. 
  According to GMX Manual page 62, using RB function implies exclusion of 1-4 LJ interactions between the first and last atom of the dihedral, which means, I should turn off the 1-4 vdw term while retaining the 1-4 coulomb term. However, I haven't found the way of doing so. If I deleted the [pairs] block in the topology file, all 1-4 interactions including 1-4 coulomb interaction would be deleted.
  Could anyone who knows key to this problem give me some help? Thanks in advance!

Yang Xunjie

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