<br><br><div><span class="gmail_quote">On 11/11/05, <b class="gmail_sendername">David</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
On Fri, 2005-11-11 at 16:53 -0500, Michael Shirts wrote:<br>> If you are mutating one atom A->B, there is no need to use soft core,<br>> as there is no problem with singularities. Actually, it would<br>> probably make things worse. I'd stick with linear interpolation in
<br>> the A and C parameters (i.e., where U(r) = A/r^6-C/r^12 -- this will<br>> likely work better than linear interpolation in epsilon and sigma, as<br>> the "core" that is excluding water will change less rapidly.
<br><br>In principle correct but H usually does not have LJ, so he is growing a<br>LJ particle here. In that case Soft-core is needed.</blockquote><div><br>
Yes, I agree with David on this one, unless he's using hydrogens which already have LJ. <br>
<br>
It would be relatively simple to check -- if indeed there are problems
he should see shot-like noise on his dv/dlambda time series absent
soft-core, and the distribution of dv/dlambda should be decidedly
non-gaussian. Things should look much better with soft core. On the
other hand, if there are no problems, both should look OK.<br>
<br>
David<br>
<br>
</div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">><br>> Also, with a change like this, I would highly suggest not using a slow
<br>> growth type simulation. As has been pointed out, hysteresis is not<br>> your friend. Instead, run a number of equilibrium simulations at<br>> intermediate with no change in lambda. Collect the average <dH/dL>,
<br>> and numerically integrate. Changing A->B, the curve should be fairly<br>> smooth, allowing for higher order integration techniques, and fewer<br>> points. I bet 5-10 will be sufficient.<br>><br>> Best,
<br>> Michael Shirts<br>> Research Fellow<br>> Columbia University<br>> _______________________________________________<br>> gmx-users mailing list<br>> <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org
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