yes it will...<br><br><div class="gmail_quote">On Fri, May 6, 2011 at 11:02 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;">
Cheers Sikandar<br>
<br>
I take it that because combination rule 3 (provide sigma and epsilon) is<br>
stated gromacs assumes that all values in nonbonding parameters are<br>
sigma and epsilon. I know this tp be tru for the atomtypes but does it<br>
filter down to all intermolecular interactions.<br>
<div class="im"><br>
Cheers<br>
<br>
Gavin<br>
<br>
Sikandar Mashayak wrote:<br>
</div><div class="im">> Yes, since sigma and epsilon are zero for VS then interactions between<br>
> and VS-VS and VS-(any other atom) would result in zero force. Since<br>
> you explicitly define the interaction between VS-C3, combination rule<br>
> won't be used and C6(VS_C3) and C12(VS_C3) will be computed as per<br>
> sigma(VS_C3) epsilon(VS_C3) you defined under [nonbond_params]<br>
><br>
> cheers<br>
><br>
> sikandar<br>
><br>
> On Fri, May 6, 2011 at 9:03 AM, Gavin Melaugh <<a href="mailto:gmelaugh01@qub.ac.uk">gmelaugh01@qub.ac.uk</a><br>
</div><div><div></div><div class="h5">> <mailto:<a href="mailto:gmelaugh01@qub.ac.uk">gmelaugh01@qub.ac.uk</a>>> wrote:<br>
><br>
> Am I correct in saying now, from the following topology (exerpts),<br>
> 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<br>
> 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>
> ;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>
> 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>
><br>
> --<br>
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