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<br><br>> Date: Wed, 16 Sep 2009 01:58:02 +1000<br>> From: Mark.Abraham@anu.edu.au<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] question about using new potential in groamcs<br>> <br>> 青 叶 wrote:<br>> > Hello everybody:<br>> > I have read GROMACS' manual and found that the non-bond interaction in GROAMCS is describled as Coulomb term add A/r^12 -B/r^6 which is named Lennard-Jones term, but recently I have read some papers which use a effective-two-body potential to describle the non-bond interaction in the GROAMCS MD simulation, and this potential works much better in dealing with transition metal ion-water system, in this potential, non-bond interaction between ion and O atom in water molecular is describled as follow:<br>> > V(r)=A/r^4+B/r^6+C/r^8+D/r^12+E*exp(-F*r)+coulomb term; <br>> > where the A,B,C,D,E and F are parameters which can be obtained by fitting the potential energy surface c
alculated from Ab initio method. r is the distance between the ion and O atom in water molecular, the interaction between the ion and H atom in water molecular has the similar form.<br>> > So my question is how to modify the GROAMCS in order to simulate dynamic course by using this new potential instead of the default L-J interaction. I have tried to find the solution in internet, but so far I still have no idea on this problem, can anybody help me on this problem, I will be very, very grateful for your help.<br>> <br>> GROMACS allows the user to supply a tabulated function in r for either <br>> bonded or non-bonded interactions. See the manual for details and <br>> $GMXLIB/gromacs/top/*xvg for examples here. Assuming you can cast the <br>> ion-O interaction and the ion-H interaction in the same functional form <br>> your problem might be simple. At worst, you might need to look up <br>> different tables for ion-O and ion-H interactions, and
this would <br>> probably need a code modification.<br>> <br>> Mark<br><br>No, you don't need code modification.<br>There are two ways around this.<br><br>1) Put O and H in different energy groups, then you can supply different tables,<br>but you will loose the water optimization (slower simulations).<br><br>2) Use C6=1, C12=0 for ion-O and C6=0,C12=1 for ion-H<br>then you can fill the dispersion table with the ion-O interaction and the repulsion<br>table with the ion-H interaction.<br><br>Berk<br><br><br /><hr />See all the ways you can stay connected <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>to friends and family</a></body>
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