[gmx-users] Free energy of discharging and then recharging not zero

[Robert Johnson]

Hi Maik,
That's exactly what I'm attempting to do...morph G to A etc. All I'm
doing here is turning off the charges of G and then turning them on
again. Wouldn't you do this anyway in the morph step? Wouldn't the
process go something like: Turn off charges -> Morph LJ parameters ->
Turn on charges.

It seems like I've got to be doing something wrong. I can't believe
that simply turning off/on the charges would drastically perturb the
entire system and prevent convergence.
Bob


On Thu, May 8, 2008 at 6:12 AM, Maik Goette <mgoette at mpi-bpc.mpg.de> wrote:
> Hi Robert
>
>  Sounds familiar to me. I also tried to compute free energy differences by
> letting whole bases appear/disappear. I ran into the same problems and
> haven't found a solution yet. Probably the perturbation is too large to gain
> converged results. My solution was stopping those simulations.
>  This doesn't sound promising, I know, but actually, I fear, there is no
> proper solution. Maybe you should morph G to A or T to C or something like
> that, where just a few atoms have to be perturbed.
>
>  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,
> > I'm trying to calculate the free energy of binding of DNA bases on a
> > carbon nanotube. I'm running some tests to make sure that I'm doing
> > everything correctly. One thing I tried was turning off all the atom
> > charges of the DNA base and then turning them back on again.
> > Theoretically, the free energy changes of these two processes should
> > be equal and opposite and thus sum to zero. However, this is not what
> > I'm finding.
> >
> > For guanine, I get a free energy change of 648 kJ/mol and -618 kJ/mol
> > for turning off and turning on the charges, respectively. Obviously,
> > they are not equal by 30 kJ/mol, which seems pretty big. I have done
> > some error estimation using the g_analyze -ee program. One thing I
> > find strange is that the error estimates in dV/dl for TURNING ON the
> > charges is large (over 2) and do not even converge for a 7.5 ns
> > simulation. In contrast, the error in dV/dl for TURNING OFF the
> > charges converges extremely quickly (using small block sizes of 50 or
> > less) and is smaller at 0.3. So it seems like I have some sampling
> > problems with the TURNING ON portion. Is there some reason why you
> > must sample a longer trajectory when turning on the charges?
> >
> > I'm following the procedures of
> > http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial
> >
> > Does anyone know the reason for the discrepancy between these two
> > (seemingly identical) processes?
> >
> > Thanks,
> > Bob
> >
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