[gmx-users] some things I am wondering

zpxu zp.xu at mf.mpg.de
Wed Aug 21 13:44:13 CEST 2002

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.
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