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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>Charge group neutrality is not an issue when you use PME.<br><br>In Gromacs 4.0 grompp would print the following message:<br></div>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.<br>For efficiency and accuracy, charge group should consist of a few atoms.<br>For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.<br><br>Simply follow this rule which groups a few atoms which are close in space.<br><br><br><hr id="stopSpelling">> Date: Mon, 26 May 2008 23:04:55 +1000<br>> From: Mark.Abraham@anu.edu.au<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Max #atoms in a charge group: 68 > 64<br>> <br>> Samuel Coulbourn Flores 花山 wrote:<br>> > So, is it generating the charge groups based on residue numbering?<br>>
; <br>> I said to look at your .itp/.top file... below you've pasted your .pdb <br>> file. I can't tell what your charge groups look like...<br>> <br>> > Can <br>> > I solve the problem by just editing the residue number column such that <br>> > the ligand is now composed of two "residues"? If not, how should I <br>> > specify how the molecule is to be broken up into charge groups? How <br>> > strict is the requirement that the charge be an integer? It seems <br>> > unlikely that any subset of the molecule will have net integer charge.<br>> <br>> That all depends how you generated the topology in the first place.<br>> <br>> Non-integral charge-groups with group-based cut-offs will make strict <br>> energy conservation difficult/impossible, though whether that has much <br>> effect depends on other stuff. I've no idea if this 64-atom limit is <br>> just a weird genion thing, or a problem you'll see with mdr
un too...<br><br>This is an mdrun limitation.<br>The exclusions for neighbor searching are set with flags in an unsigned long,<br>which is 64 bits.<br><br>In 4.0 grompp will give a warning for charge groups larger than 10 atoms.<br><br>Berk.<br><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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