<!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 name=GENERATOR content="MSHTML 8.00.6001.18247">
<STYLE></STYLE>
</HEAD>
<BODY bgColor=#ffffff>
<DIV><FONT size=2 face=Tahoma>Hi, all,<BR> I am doing shell molecular
dynamics and I have read the sw.itp. Now my question is:<BR>1. For the shell
"atom", what element should be used in .pdb file, since the 77-78th digits of
pdb file is element symbol ?<BR>2. What does the 1 in [ polarization ] part mean
in sw.itp? <BR>3. Is it reasonable to set initial position of shell arbitrally
and let energy minimization to find the optimum position for shell?<BR>I also do
not understand [ exclusion ] part:<BR>; iatom excluded from interaction with
i<BR>1 2 3 4 5<BR>2 1 3 4 5<BR>3 1 2 4 5<BR>4 1 2 3 5<BR>5 1 2 3 4<BR>For the
first line, does that mean that the interaction of 2, 3, 4 and 5 with 1 is
excluded? If so, this table will exclude all the interactions. Is it
right?<BR>Thank you in advance.<BR>Shuangxing Dai</FONT></DIV></BODY></HTML>