<html>
<head>
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Tahoma
}
--></style>
</head>
<body class='hmmessage'>
Yes.<br><br>The pow function is expensive though. The code will run much faster<br>if you can use rinvsix, such as check for 2*rinvsix > c6/c12.<br>(I forgot the factor 2 in my previous mail).<br><br>Berk<br><br>> From: makoto-yoneya@aist.go.jp<br>> To: gmx-users@gromacs.org<br>> Date: Tue, 11 Jan 2011 10:10:56 +0900<br>> Subject: [gmx-users] truncated LJ potential<br>> <br>> Dear Berk:<br>> <br>> Thanks again for the further reply.<br>> <br>> >> The LJ potential and force code in the above looks like in the c6-c12<br>> form<br>> >> not in epsilon-sigma one.<br>> >> The LJ potential modification I'd like to try is based on the epsilon-<br>> >> sigma form and the mixing rule is the Lorents-Bertelot's one.<br>> >> Could you kindly tell me the LJ potential and force routine in the<br>> epsilon-<br>> >> Sigma form.<br>> ><br>> >There is no such code.<br>> ><br>> >You can simply check for rinvsix > c6/c12<br>> <br>> Is it means that the LJ potential in epsion-sigma form (with the<br>> Lorents-Bertelot <br>> mixing rule) is evaluated after the coversion into c6-c12 form in GROMACS?<br>> Then, may I evaluate the modified LJ potential:<br>> <br>> > > V(r)<br>> > > = 4*epsilon*{ (sigma/r)^(12) - (sigma/r)^6 + (1/4) } for r<=<br>> > > 2^(1/6)*sigma<br>> > > = 0 for r> 2^(1/6)*sigma<br>> <br>> with translated into the equivalent c6-c12 form:<br>> <br>> V(r)<br>> = (c12/r)^(12) - (c6/r)^6 + (c6/2)*(c6/2*c12) for r<= (2*c12/c6)^(1/6)<br>> = 0 for r > (2*c12/c6)^(1/6)<br>> <br>> in the following routines.<br>> > > You can also set the environment variable nb_generic.c and modify<br>> > > src/gmxlib/nonbonded/nb_generic.c, but might lead to somewhat<br>> > > slower simulations.<br>> <br>> If my understanding in the above would correct, I'll try that.<br>> <br>> Thank you for advance.<br>> <br>> Makoto Yoneya, Dr.<br>> http://staff.aist.go.jp/makoto-yoneya/<br>> <br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br> </body>
</html>