Bob, Right, exactly. What I recommend is to turn off the charges with sc_alpha set to zero, and only use sc_alpha nonzero when changing VdW interactions.
See for example Guideline 4 here: http://www.alchemistry.org/wiki/index.php/Best_Practices (FWIW, this is our attempt to compile some general "best practices" for free energy calculations, but it's still in progress. It's publicly editable). David On Jan 25, 2008 3:26 PM, Robert Johnson <[EMAIL PROTECTED]> wrote: > Thanks David, > Since I'm turning off the VdW parameters as a second step, there > really isn't any reason to use the soft core potentials when turning > off the charges right? Thus, sc_alpha should be set to zero when > turning off charges? > Thanks, > Bob > > On Jan 25, 2008 5:38 PM, David Mobley <[EMAIL PROTECTED]> wrote: > > It will only be smooth if you don't use soft core (i.e. sc-alpha =0 ). > > > > Best, > > David Mobley > > http://www.dillgroup.ucsf.edu/~dmobley > > > > > > On Jan 25, 2008 12:40 PM, Robert Johnson <[EMAIL PROTECTED]> wrote: > > > Hello everyone, > > > As I mentioned in a previous post, I'm trying to compute the free > > > energy of binding of a DNA base on a carbon nanotube. My system > > > consists of a single DNA nucleotide (base, sugar, phosphate group) on > > > a rigid carbon nanotube in aqueous solution. A single Na+ counterion > > > is also included for charge neutralization. I'm proceeding with this > > > by computing the free energy associated with the following > > > transformations: > > > > > > Water + Nanotube + DNA + Na+ -> Water + Nanotube + Nothing > > > Water + DNA + Na+ -> Water + Nothing > > > > > > For each of these transformations I FIRST turn off the charges on the > > > base and counterion over a set of 5 lambda values (0.0, 0.25, 0.5, > > > 0.75, 1.0). From literature and other posts on the GMX mailing list, > > > it seems like this small set of values should be adequate because > > > dG/dlambda tends to be pretty smooth for discharging the molecule. > > > > > > Unfortunately, that doesn't seem to be the case in my system. Here is > > > a table of the dG/dlambda values I get from running 5 ns trajectories > > > of my system: > > > > > > lambda <dG/dlambda> > > > 0.0 6211.105 > > > 0.25 1055.254 > > > 0.5 1230.675 > > > 0.75 1128.359 > > > 1.0 756.2904 > > > > > > If you plot this you will see a large drop from lambda=0 to 0.25. Then > > > dG/dlambda increase slightly from lambda=0.25 to 0.5 and then smoothly > > > decreases after that. This seems like a pretty strange result. Also, > > > it seems that something weird is going on around lambda=0. If I > > > compute dG/dlambda for lambda=0.05, I get something around 1200-1300, > > > which is again a very sharp decrease from the value of 6211.105 I get > > > at lambda=0. Thus, it doesn't seem like simply adding more lambda > > > values is going to help me. > > > > > > Here are the values I'm using for the free energy calculation: > > > free_energy = yes > > > init_lambda = 0.05 > > > delta_lambda = 0 > > > sc_alpha = 0.5 > > > sc_power = 1 > > > sc_sigma = 0.3 > > > > > > Also, here is an excerpt from my topology file: > > > [ atoms ] > > > 1 P 1 DG P 1 1.1659 30.9700 > > > P 0.0000 30.9700 > > > 2 O 1 DG O1P 1 -0.7761 16.0000 > > > O 0.0000 16.0000 > > > 3 O 1 DG O2P 1 -0.7761 16.0000 > > > O 0.0000 16.0000 > > > > > > I'm not perturbing any of the bonding interactions or VdW parameters - > > > I'm just turning off all charges on the molecule. > > > > > > Does anyone have any ideas or suggestions about how this can be improved? > > > > > > Thanks, > > > Bob Johnson > > > _______________________________________________ > > > gmx-users mailing list gmx-users@gromacs.org > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at http://www.gromacs.org/search before posting! > > > 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 gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > 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 gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
