[gmx-users] some things I am wondering

[zpxu]

and I will be very happy if you tell me why.
1) in the section [moleculetype], we must specify the value of nrexcl(excluded numbers)
    In my understanding, non-bond interactions within the number of bonds are excluded.
    so if using bond+angle+dihedral, nrexcl will be set to be 3, and if using bond+angle only,
    I need only set it to be 2, it is right? for the result of 2 and 3 are quite different.
2) why we must specify the atom number with bond, and angle interaction in the [bonds] and [angles]
   section? because in some cases, if the atoms have great displacement, the bond and angle list 
   have to be updated, and so I guess the GROMACS have the bond list finding function. but why we 
   must specify it at the topological file?
thank for answering suck fundamental questions.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20020821/5e49dc24/attachment.html>