My take is that it is preferable to partition your vdW and charge changes into two separate calculations, as the soft core settings that work well for the vdW portion make the charging portion a more "difficult" transformation than normal, and the settings that work well for charging make the vdW portion "difficult". In my experience, I can get by with fewer lambda values by doing the calculation in two portions than I would need to do it all together.
Also, I find that the parameters which work best for vdW are alpha=0.5 and sc-power=1, which is what Michael Shirts had come up with as close to optimal. When I deviate from those, the dv/dlambda curve gets a lot less smooth and I get much larger errors -- especially if I go up above alpha=1 (and even more so at alpha=2). If I were you, I would probably set up a test calculation where you are only changing vdW interactions, and then play a bit with the alpha (and lambda spacing) to see what gives you the smoothest dv/dlambda curve for which you need the fewest lambda values. Then you can add back in the charge modification, if you like, and see if this messes up the curve a lot. If so, then do the charges in a separate calculation before/after changing the vdW (depending on what exactly you're doing with the charges). David On 5/29/06, Berk Hess <[EMAIL PROTECTED]> wrote:
>From: [EMAIL PROTECTED] >Reply-To: Discussion list for GROMACS users <[email protected]> >To: [email protected] >Subject: [gmx-users] TI, sampling, sc_power, and sc_alpha >Date: Fri, 26 May 2006 12:36:20 -0700 (PDT) > >Greetings once again fellow Gromacs-users, > >I have seen a substantial and disturbing change in calculated free energy >differences >between systems run with Gromacs 3.3 and Gromacs 3.3.1. I am trying to >determine if >these differences are due to the new software, new parameters, insufficient >sampling, or >something else, and I don't have enough computer time to investigate every >possible >combination. I turn to the list for insight. I had implemented the alpha=1 option in 3.3 and set it as default, since it seemed to produce "better" dH/dl curves, especially for LJ-only perturbations. Only some time after the 3.3 release I realized that this might cause a lot of trouble as people probably did not realize that the default alpha value had changed. I apologize for having caused such inconveniences. To prevent such mistakes I have set default value to zero in 3.3.1, which is not allowed, so people are forced to think about alpha. The problem is that there is not (yet) an optimal soft-core dependence for combined charge/LJ perturbations. For LJ only alpha=1 is quite optimal. But for charge perturbations alpha=1 causes an extremely sharp peak exactly at lambda=0 (or 1). For alpha=2 this peak at zero shift to values slighlty above zero and becomes less sharp, here you have to sample the both slopes of the peak. With alpha=1 you need a very non-linear lambda distribution with a very fine spacing close to 0. With alpha=2 you also need a fine spacing at 0, but probably also in the middle where the particles start overlapping. I would guess that especially alpha=1 can give an enourmous error if you only used 21 evenly spaced points. Adding points at 0.01 and 0.02 from lambda=0 and/or 1 could help a lot. Berk. _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
