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<br><br>> Date: Mon, 10 Jan 2011 14:04:34 +0100<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] truncated LJ potential<br>> <br>> On 2011-01-10 13.39, Makoto Yoneya wrote:<br>> > Dear GROMACS experts:<br>> ><br>> > I'd like to use a modified Lennard-Jones potential (smoothly truncated at<br>> > only the repulsive part) in the following.<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>> > Which routine should I change to realize this LJ potential modification<br>> > without any side effects.<br>> > I'd like to use this in some coarse-grained simulations.<br>> > Sorry if this is a FAQ.<br>> ><br>> > Thank you for advance.<br>> ><br>> > Makoto Yoneya, Dr.<br>> > AIST, Tsukuba<br>> > JAPAN<br>> > http://staff.aist.go.jp/makoto-yoneya/<br>> ><br>> Dear Makoto,<br>> <br>> please look into gromacs' table potential functionality, it is described <br>> in the manual, and you won't have to program anything<br>> UNLESS the sigma is different for different atom pairs, in that case I'm <br>> not sure if it will work.<br><br><br>You can make different tables for interactions between groups of atoms with<br>different sigma's by putting these groups in different energy groups,<br>but this might get tedious.<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>Berk<br><br>                                            </body>
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