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<DIV><FONT face=Verdana size=2>Hi Berk,</FONT></DIV>
<DIV><FONT face=Verdana size=2></FONT> </DIV>
<DIV><FONT face=Verdana size=2>Should the total charge for one charge group
be necessarily an integer, such as 0, 1, -1?</FONT></DIV>
<DIV><FONT face=Verdana size=2></FONT> </DIV>
<DIV><FONT face=Verdana size=2>If I understand correctly, the answer is yes.
However in this case, the large charge group always happens
except opls-aa force field.</FONT></DIV>
<DIV><FONT face=Verdana size=2></FONT> </DIV>
<DIV><FONT face=Verdana size=2>regards,</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Verdana size=2>
<HR>
</DIV></FONT>
<DIV><FONT face=Verdana><FONT size=2><STRONG>发件人：</STRONG> Berk
Hess</FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>发送时间：</STRONG>
2008-11-20 00:21:07</FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>收件人：</STRONG> Discussion list for
GROMACS users</FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>抄送：</STRONG> </FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>主题：</STRONG> RE: [gmx-users] large
charge group</FONT></FONT></DIV>
<DIV><FONT face=Verdana size=2></FONT> </DIV>
<DIV><FONT face=Verdana size=2>Hi,<BR><BR>The charge groups "only" affect the
neighbor searching,<BR>which in practice means they affect everything.<BR><BR>In
Gromacs atoms in two different charge groups will only interactions<BR>when the
center of geometry of the two charge groups is within rlist.<BR><BR>The worst
case scenario, which has happend to several people, is:<BR>A molecule with a
radius of about 0.5 nm is one charge group.<BR>If the cut-off is 1 nm, two
molecules will only really start interacting<BR>when they already
overlap.<BR><BR>In 4.0 I put a check on large charge groups.<BR>If you have
charge groups of more than 10 atoms, grompp will now<BR>warn you with:<BR>"The
largest charge group contains %d atoms.\n"<BR>"Since atoms only see each other
when the centers of geometry of the charge groups they belong to are within the
cut-off distance, too large charge groups can lead to serious cut-off
artifacts.\n"<BR>"For efficiency and accuracy, charge group should consist of a
few atoms.\n"<BR>"For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2,
CO, etc.\n",<BR><BR>Berk<BR><BR>> Date: Wed, 19 Nov 2008 10:01:01
-0600<BR>> From: sunnytov@gmail.com<BR>> To: gmx-users@gromacs.org<BR>>
Subject: [gmx-users] large charge group<BR>> <BR>> Hello All<BR>>
<BR>> Recently I have figured out the biggest problem that made my system
unstable.<BR>> I have parameterized a molecule pretty similar to octane. A
single<BR>> charge group used to be assigned to this molecule. With 1 nm
cut-off<BR>> distance for LJ interaction and the direct space for
electrostatic<BR>> interaction, the system underwent severe volume
fluctuation and at the<BR>> end crashed due to enormously large short range
coulomb interaction<BR>> energy. The problem was temporarily resolved by
using greater cut-off<BR>> distance such as 1.4 nm. But this fixation was not
perfect when I put<BR>> this molecule into more complex system. Regardless of
the cut-off<BR>> distance even to 1.8 nm did not solve the problem. The
simulation<BR>> always terminated due to large coulomb energy even though no
direct<BR>> contact or any weird structure was observed at that
snapshot.<BR>> <BR>> With the help of many experts, I have made a single
charge group into<BR>> three smaller charge group, which magically fixed all
the problem that<BR>> I have had for almost 2 years. I know that charge group
is only used<BR>> for neighbor search. Can anybody tell me how the size of
charge group<BR>> can influence the interaction between atoms depending on
the<BR>> complexity of the system and cut-off distance??<BR>> <BR>>
Thank you in advance<BR>> <BR>> Sunjoo<BR>>
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