<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:garamond, 'new york', times, serif;font-size:12pt"><div></div><div>Thanks. But I've read the manual. It seems not solving it. The two potentials in my system are of totally different function forms. They do not just differ in the parameters. What troubles me is GROMACS seems not to be able to support two function forms simultaneously for van der Waals interactions. <br> </div><div style="font-family:garamond, new york, times, serif;font-size:12pt"><div style="font-family:arial, helvetica, sans-serif;font-size:13px"><br>On 2010-03-31 21.53, hong bingbing wrote:<br>> Thanks, David.<br>><br>> Let me simplify my system. It includes A and B molecules. The van der<br>> Waals interaction between A's is, e.g. U1(r) = -1/r cutted off at r =<br>> r_A ; and for B: U2(r) = -1/r^2, cut off at r = r_B.<br>><br>> I don't know how to handle with two potentials and
two cutoffs<br>> simultaneously.<br>><br>Read manual and online instructions about tabulated potentials in <br>gromacs. You have to specify files for each interaction pair, that is <br>AA, AB, BB, then simulate with cutoff max(r_A,r_B). Make sure the <br>potentials are continuous and smooth to at least the cutoff.<br><br>><br>><br>><br>><br>> -----------------------------------<br>><br>> Dear all,<br>><br>> I'm trying to simulate multiple phases in one system. Each phase has<br>> distinct van der Waals potential form and different<br>> cutoffs from the rest. Unfortunately, I found only one van der Waals<br>> potential and one cutoff can be defined in .mdp file of one run. Did I<br>> miss some features of GROMACS? Have you encountered this problem before<br>> and could you lend a help?<br>><br>> Thank you<br>> Cynthia<br>><br>><br>><br><br><br>-- <br>David van der Spoel, Ph.D., Professor of Biology<br>Dept. of Cell & Molec. Biol., Uppsala
University.<br>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br><a ymailto="mailto:spoel@xray.bmc.uu.se" href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>-- <br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a
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