<div>Thank you for your help. I checked all the force field, all of them are with default non-bond params in LJ. So I still need to try new solution.</div>
<div>I add my non bond parameters in the .top file generated. Force field files were not changed. Then I use grompp, the error was:</div>
<div> </div>
<p style="MARGIN: 0in; FONT-FAMILY: Verdana; FONT-SIZE: 11pt" lang="zh-CN">'[ nonbond_params ]'</p>
<p style="MARGIN: 0in; FONT-FAMILY: Verdana; FONT-SIZE: 11pt" lang="zh-CN">Invalid order for directive nonbond_params</p>
<div>Rather confused by setting up Buckingham potential parameters... </div>
<div>Thank you very much!<br><br></div>
<div class="gmail_quote">2009/2/26 Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>></span><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div>Hi,<br><br>But do you need any other parameters than zinc and oxide?<br>If not, you can simply remove all other parameters.<br>If you need other atoms as well, you will need to find<br>a consistent force field, probably or completely LJ<br>
or completely Buckingham.<br><br>Berk <br><br>> Date: Thu, 26 Feb 2009 09:22:26 +1100<br>> From: <a target="_blank" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>
<div class="im"><br>> To: <a target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> Subject: Re: [gmx-users] combination rules -- the part aboutthecombinationrules<br>> <br></div>
<div>
<div></div>
<div class="h5">> Shuangxing Dai wrote:<br>> > Yes, "add parameters for crystalline zinc oxide, which require <br>> > Buckingham nonbonded interactions", that is what I am doing. I think I <br>> > have changed all the necessary parts for the Buckingham potential. Is <br>
> > there any direct way to accomplish my goal?<br>> <br>> No, because it's not a reasonable goal. Your new atomtypes are talking a <br>> different vdW "language". That doesn't work.<br>> <br>
> > Since in ffgmxnb.itp, all the nonbond_params are LJ if the default type <br>> > is 1. I only changed the parameters for Zn and O to Buckingham <br>> > parameters. And you said "add your functions in the right form in your [ <br>
> > molecule ] section" , I cannot find the right place to change.<br>> <br>> Chapter 5 of the manual.<br>> <br>> > And what <br>> > force field to choose if not ffgmx?<br>> <br>> That's your homework I'm afraid. You'll have to read the literature.<br>
> <br>> Mark<br>> _______________________________________________<br>> gmx-users mailing list <a target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a target="_blank" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a target="_blank" href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to <a target="_blank" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a target="_blank" href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br><br></div></div>
<div class="im">
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</blockquote></div><br><br clear="all"><br>-- <br>Shuangxing Dai<br>