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

[Justin A. Lemkul]

Perhaps a naive question, but which version of Gromacs are you using?  Such
issues are well-known in 3.3.1, but have been fixed in the most recent release
(3.3.3).

-Justin

Quoting Robert Johnson <bobjohnson1981 at gmail.com>:

> 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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> > >
> > >
> >
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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