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 [email protected] > 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 [email protected] 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
