[gmx-users] Rugged dG/dlambda when turning off charges
bobjohnson1981 at gmail.com
Sat Jan 26 00:26:37 CET 2008
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?
On Jan 25, 2008 5:38 PM, David Mobley <dmobley at gmail.com> wrote:
> It will only be smooth if you don't use soft core (i.e. sc-alpha =0 ).
> David Mobley
> On Jan 25, 2008 12:40 PM, Robert Johnson <bobjohnson1981 at gmail.com> 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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