<div>Yes, "add parameters for crystalline zinc oxide, which require Buckingham nonbonded interactions", that is what I am doing. I think I have changed all the necessary parts for the Buckingham potential. Is there any direct way to accomplish my goal? </div>
<div>Since in ffgmxnb.itp, all the nonbond_params are LJ if the default type is 1. I only changed the parameters for Zn and O to Buckingham parameters. And you said "add your functions in the right form in your [ molecule ] section" , I cannot find the right place to change. And what force field to choose if not ffgmx? </div>
<div>Thank you very much.<br></div>
<div class="gmail_quote">2009/2/22 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div class="Ih2E3d">Shuangxing Dai wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">No. I only changed 3 lines in ffgmxnb.itp. But there are hundreds of lines of error informaion like this:<br>
ERROR 77 [file ffgmxnb.itp, line 144]:<br> Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR)<br></blockquote><br></div>Sure, this is predictable. This force field's files come filled with LJ functions, and the default pertains to all of them. So you can either have one form or the other.<br>
<br>The issue is that if the force field generates the functions for interactions based on the atom types, you can't mix the two types, since the result is not defined. Sorry I didn't pick this up the first time, but if you'd had a descriptive header "I'm trying to add parameters for (?) crystalline zinc oxide, which require Buckingham nonbonded interactions" then your strategy problem would have been obvious.<br>
<br>I'm guessing here, but you may not be constrained by the default type if you just add your functions in the right form in your [ molecule ] section. This means you don't need to modify the force field files at all! However you will need to supply a non-bonded interaction manually for any new atom type with every atom type in your system. Those also seems likely to be undefined.<br>
<br>You also shouldn't be using ffgmx for a new simulation, because it has been deprecated for years now.
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<div class="Wj3C7c"><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>
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