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

[Robert Johnson]

I'm continuing to look at this stuff. Just a quick sanity check....at
lambda=0.5 I should be getting equal and opposite values for <dV/dl>
for the forward and reverse reactions. Is that correct?
Thanks,
Bob


On Thu, May 8, 2008 at 11:56 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> 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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>
>
>
> ========================================
>
> 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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