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<br><br>> Date: Fri, 27 Mar 2009 09:56:02 +1100<br>> From: Mark.Abraham@anu.edu.au<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] How to add another electrostatic summation method in Gromacs<br>> <br>> Shuangxing Dai wrote:<br>> > Thank you for your help. I attached the page of the form of potential. <br>> > The equation (5.13) gives all the potential energy of neighbours of one <br>> > ion in a truncation sphere. Rc is cut-off. Since this potential depends <br>> > on all the neighbours in a cut-off distance, I cannot give the pair <br>> > interaction because in this method, only the total potential energy of <br>> > one ion maks sense. In Ewald summation, both the real space and <br>> > reciprocal space summation can be written as the summation of pair <br>> > potential. But in wolf, I cannot do that.<br>> <br>> It looks separable into a double sum over atom pairs from within a <br>> cutoff, since the value of that limit is constant.<br>> <br>> > Since I cannot use Ewald without peoriodical boundary conditions while <br>> > this Wolf method can, so I cannot simply use Gromacs to do my <br>> > simulation. The question is which files needed to be modified if I want <br>> > to add a new one? Is there any direct way? Or I should read all the <br>> > whole code?<br>> <br>> You can start by reading the kernel code generated by mknb during the <br>> make process and found in src/gmxlib/nonbonded/nb_kernel. If you play <br>> with the flags to mknb you can get comments embedded in the C files. <br>> Find the one that does Ewald without table lookups and consider how <br>> you'd need to change it to suit your needs.<br>> <br>> Mark<br><br>Note that in 4.0 there are now also plain c loops:<br>src/gmxlib/nonbonded/nb_generic.c<br>which are easy to modify.<br>You will need to set the env var GMX_NB_GENERIC to use them.<br><br>Berk<br><br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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