[gmx-users] Rugged dG/dlambda when turning off charges

[Maik Goette]

The point is: You want to do a severe perturbation. May I inform you, 
that I tried morphing base pairs for 3 years and now quitted? ;)
Anyway, if you have such a strong perturbation, you should think about a 
different setup, like softcore for vdw and harcore for qq.

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Robert Johnson 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
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