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Hi,<br><br>This is not a decision, but a limitation of the grompp code.<br>I have fixed this in the git release.<br><br>Simply editing the charge group numbers by hand to make them all different<br>should work.<br><br>Berk<br><br>> Date: Mon, 3 May 2010 10:22:54 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] cgnr in top file<br>> <br>> <br>> <br>> Erik Marklund wrote:<br>> > True. I guess gromacs groups together the terminal hydrogens, overriding <br>> > the original force field parameters. Can't say why that decision was <br>> > made, but it will influence your simulation very little.<br>> <br>> I think there was a bug report some time ago involving virtual sites on the <br>> termini of all-atom force fields causing a crash when the terminus crossed a <br>> periodic boundary. Could be related to that, although I can't remember the <br>> exact progress behind the fix.<br>> <br>> -Justin<br>> <br>> > <br>> > Erik<br>> > <br>> > leila karami skrev:<br>> >> Dear Erik<br>> >> <br>> >> you said Amber03 was not parameterized with charge groups and last <br>> >> column in your rtp entry holds the chargegroup numbers. but<br>> >> cgnr column in my top file does not looks just like it. in case of H1, <br>> >> H2 and H3.<br>> >> <br>> >> / H1 amber99_17 0.16420 2<br>> >> // H2 amber99_17 0.16420 3<br>> >> // H3 amber99_17 0.16420 4<br>> >> // // /. that's ok. but why<br>> >> <br>> >> /and my top file is as follow :<br>> >> // // // <br>> >> nr type resnr residue atom cgnr charge mass <br>> >> // //2 amber99_17 1 NGLY H1 2 0.1642 <br>> >> 1.008 // 3 amber99_17 1 NGLY H2 2 <br>> >> 0.1642 1.008 // 4 amber99_17 1 NGLY H3 <br>> >> 2 0.1642 1.008 // /<br>> >> thanks for your attention <br>> > <br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.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 />New Windows 7: Find the right PC for you. <a href='http://windows.microsoft.com/shop' target='_new'>Learn more.</a></body>
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