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
