<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META content="text/html; charset=iso-8859-1" http-equiv=Content-Type>
<META content="MSHTML 5.00.3315.2870" name=GENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=#ffffff>
<DIV><FONT face=Arial size=2>and I will be very happy if you tell me
why.</FONT></DIV>
<DIV><FONT face=Arial size=2>1) in the section [moleculetype], we must specify
the value of nrexcl(excluded numbers)</FONT></DIV>
<DIV><FONT face=Arial size=2> In my understanding, non-bond
interactions within the number of bonds are excluded.</FONT></DIV>
<DIV><FONT face=Arial size=2> so if using bond+angle+dihedral,
nrexcl will be set to be 3, and if using bond+angle only,</FONT></DIV>
<DIV><FONT face=Arial size=2> I need only set it to be 2, it
is right? for the result of 2 and 3 are quite different.</FONT></DIV>
<DIV><FONT face=Arial size=2>2) why we must specify the atom number with bond,
and angle interaction in the [bonds] and [angles]</FONT></DIV>
<DIV><FONT face=Arial size=2> section? because in some cases, if the
atoms have great displacement, the bond and angle list </FONT></DIV>
<DIV><FONT face=Arial size=2> have to be updated, and so I guess the
GROMACS have the bond list finding function. but why we </FONT></DIV>
<DIV><FONT face=Arial size=2> must specify it at the topological
file?</FONT></DIV>
<DIV><FONT face=Arial size=2>thank for answering suck fundamental
questions.</FONT></DIV></BODY></HTML>