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No, it does not need to be integer.<br>With PME it does not matter at all.<br>With cut-off or reaction-field it is better to have neutral<br>charge groups when possible, but not at the cost<br>of making enormous charge groups.<br><br>Charge groups should preferable consist of 2, 3 or 4 atoms<br>which are very close together in space.<br><br>Berk.<br><br><hr id="stopSpelling">Date: Thu, 20 Nov 2008 09:29:46 +0800<br>From: qiaobf@gmail.com<br>To: gmx-users@gromacs.org<br>Subject: Re: RE: [gmx-users] large charge group<br><br>
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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">
</font><hr>
</div><font face="Verdana" size="2"></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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