<div>Got it, Thank you, Mark!</div><div>Best!</div><div>Xueming<br><br></div><div class="gmail_quote">On Wed, Jan 4, 2012 at 1:18 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid" class="gmail_quote"><div class="HOEnZb"><div class="h5">On 4/01/2012 4:43 PM, XUEMING TANG wrote:<br>
<blockquote style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid" class="gmail_quote">
Hello<br>
<br>
I am trying to adjust compound LJ parameter in oplsaa (sigma&epsilon) and also in Gromos (C6 and C12) forcefield for comparison. The original ffnonbonded.itp file in oplsaa.ff has no pair potential listed. While the original ffnonbonded.itp file in gromos**.ff listed all the pair potentials. If I change one atom potential, do I need to do anything to generate the new pair potential before running a simulation in opls-aa force field? Or how to generate the pair potentials? While for the case of gromos forcefield, the forcefield.itp file shows no pair potential will be generated. Is there any automatic ways to generate the modified LJ potentials? Should I list every possible LJ pair potentials in nonbonded.itp file? It looks like some very tedious work if several atoms are going to be modified.<br>
Also, what does fudge LJ and fudgeQQ mean in forcefield.itp file? Values of those two are different for OPLS and Gromos.<br>
</blockquote>
<br></div></div>
In general, two force fields work differently and have their own idiosyncrasies that will show up in how GROMACS implements them. When modifying them, you should be sure to check the original literature and the GROMACS manual and satisfy yourself how your changes will work. You should search the manual for discussion of the use of gen-pairs and the fudge values. I don't know why the list of [ nonbond_param ] values is exhaustive - you'd think the combination rules could be used. In practice, you only need to add parameters for interactions that can occur in your system, and grompp will complain about those that it can't find.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark<br>
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