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Hi,<br><br>Is line 68 one of the lines you have added, or another one?<br><br>Berk<br><br>> From: shuangxingdai@gmail.com<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] combination rules -- the part aboutthe combinationrules<br>> Date: Sun, 22 Feb 2009 14:55:21 -0700<br>> <br>> Thank you. I have referred to the manual and changed these parts as the <br>> manual told me:<br>> in ffgmx.itp:<br>> [ defaults ]<br>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br>> 2 1 no 1.0 1.0<br>> <br>> in ffgmxnb.itp:<br>> [ nonbond_params ]<br>> ; i j func a b c6<br>> O O 2 92137.86 45.62876437 3090<br>> ZN O 2 51108.27 27.92516056 0<br>> ZN ZN 2 0 0.1 0<br>> But there is no change in the generated .top file.<br>> When I use grompp, the errors are :<br>> ERROR 1 [file ffgmxnb.itp, line 68]:<br>> Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR)<br>> Maybe somewhere else need to be changed. Anyone knows why and how?<br>> Thank you in advance.<br>> <br>> ----- Original Message ----- <br>> From: "Mark Abraham" <Mark.Abraham@anu.edu.au><br>> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>> Sent: Friday, February 20, 2009 6:02 PM<br>> Subject: Re: [gmx-users] combination rules -- the part aboutthe <br>> combinationrules<br>> <br>> <br>> > Shuangxing Dai wrote:<br>> >> Thanks for your answer. I changed the non-bond parameters in ffgmxnb.itp. <br>> >> like<br>> >> ; i j func a b c6<br>> >> Zn O 2 ... ..... .... But error occured..<br>> >><br>> >> ERROR 1 [file ffgmxnb.itp, line 270]:<br>> >><br>> >> Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)<br>> >><br>> >> ERROR 2 [file ffgmxnb.itp, line 271]:<br>> >><br>> >> Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)<br>> >><br>> >> ERROR 3 [file ffgmxnb.itp, line 272]:<br>> >><br>> >> Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)<br>> >><br>> >> I think I have indicated that the function type is 2 (means Buckingham). <br>> >> Anything else need to do with this ?<br>> ><br>> > ... specify that the default nonbonded type is not LJ? Have a look in <br>> > Chapter 5 of the manual.<br>> ><br>> >> Also, I want to fix some atoms in the boundary and specify displacement <br>> >> to some atoms, anayone knows how to do this?<br>> ><br>> > You can freeze groups of atoms, or use position restraints, or pull groups <br>> > of atoms, but you should look first in the manual for the information that <br>> > is there.<br>> ><br>> > Mark<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 www <br>> > 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>> _______________________________________________<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 />What can you do with the new Windows Live? <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>Find out</a></body>
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