Yes, since sigma and epsilon are zero for VS then interactions between and VS-VS and VS-(any other atom) would result in zero force. Since you explicitly define the interaction between VS-C3, combination rule won't be used and C6(VS_C3) and C12(VS_C3) will be computed as per sigma(VS_C3) epsilon(VS_C3) you defined under [nonbond_params]<div>
<br></div><div>cheers</div><div><br></div><div>sikandar<br><br><div class="gmail_quote">On Fri, May 6, 2011 at 9:03 AM, Gavin Melaugh <span dir="ltr"><<a href="mailto:gmelaugh01@qub.ac.uk">gmelaugh01@qub.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Am I correct in saying now, from the following topology (exerpts), that<br>
the virtual site VS will only interact with C3?<br>
I guess I don't have to give the atom indices of this interaction in the<br>
pair list which I use only for 1_4 interactions?<br>
Can I use sigma and epsilon in the nonbond_params directive like in<br>
atomtypes.<br>
<br>
;Parameter level<br>
[defaults]<br>
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br>
1 3 yes 0.5 0.5<br>
<br>
[atomtypes]<br>
<div class="im">;type mass charge ptype sigma(nm)<br>
epsilon(kjmol-1)<br>
CB 12.011000 0.000000 A 0.355000 0.292880<br>
CA 12.011000 -0.115000 A 0.355000 0.292880<br>
</div> HC 1.008000 0.115000 A 0.242000 0.125520<br>
CU 13.019000 0.265000 A 0.350000 0.334720<br>
NU 14.007000 -0.597000 A 0.325000 0.711280<br>
CH 13.019000 0.332000 A 0.385000 0.334720<br>
C3 15.035000 0.000000 A 0.390500 0.732200<br>
C2 14.027000 0.000000 A 0.390500 0.493712<br>
VS 0.0 0.0 V 0.0 0.0<br>
<br>
<br>
[nonbond_params]<br>
;i j func sigma epsilon<br>
VS C3 1 0.1 0.03153<br>
<div><div></div><div class="h5"><br>
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