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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>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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