[gmx-users] Re: Free Energy tutorial - choosing number of solvent molecules

[Fabian Casteblanco]

Hello Justin,

I am running 2,000,000 time steps for the actual MD run (4,000 ps).
Depending on how many solvent molecules I start with, I get slightly
different results.  Do you think its ok to run several different tests
and take the average?  Or perhaps take the end results of a shorter MD
run and use those as the starting coordinates for a new run?

Thanks,
Fabian


--------------------------------------------------------

Fabian Casteblanco wrote:
> Hello all,
>
> I'm running the same process from the free energy tutorial by Justin
> Lemkul...http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html.
>
> How did the number of solvent particles get chosen (in the tutorial, 210
> molecules were chosen)?   I seem to be getting slightly different

If memory serves, I reproduced what was in the original paper, but do check.

> results (ranging from as small as 200 J/mol to about 5 kJ/mol depending
> on how many molecules I choose (ranging for example from 210 ethanol
> molecules to about 610 ethanol molecules for the largest energy
> difference change of about 5 kJ).   I keep running tests to see if there
> is some sort of minimum atom number to get steady consistent numbers but
> I can't seem to find it.  When I plot for example the bar.xvg &
> barint.xvg for both sets to see where the lines don't match up, its
> usually one or two points that differ slightly which cause the free
> energies in the end to be slightly different.    I seem to be noticing
> too that the more atoms I use, the free energy gets a little bit lower.
>
> Does anybody have any experience with this?
>

How long are your simulations?  I have experienced the case (using a
water-octanol solvent mixture) where the initial configuration made a big
difference in the result, so longer simulations and multiple configurations for
the solvent were necessary to get reliable averages.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



On Thu, Jan 26, 2012 at 11:21 AM, Fabian Casteblanco
<fabian.casteblanco at gmail.com> wrote:
>
> Hello all,
>
> I'm running the same process from the free energy tutorial by Justin Lemkul...http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html.
>
> How did the number of solvent particles get chosen (in the tutorial, 210 molecules were chosen)?   I seem to be getting slightly different results (ranging from as small as 200 J/mol to about 5 kJ/mol depending on how many molecules I choose (ranging for example from 210 ethanol molecules to about 610 ethanol molecules for the largest energy difference change of about 5 kJ).   I keep running tests to see if there is some sort of minimum atom number to get steady consistent numbers but I can't seem to find it.  When I plot for example the bar.xvg & barint.xvg for both sets to see where the lines don't match up, its usually one or two points that differ slightly which cause the free energies in the end to be slightly different.    I seem to be noticing too that the more atoms I use, the free energy gets a little bit lower.
>
> Does anybody have any experience with this?
>
> Thanks.
>
> --
> Best regards,
>
> Fabian F. Casteblanco
> Rutgers University --
> C: +908 917 0723
> E:  fabian.casteblanco at gmail.com
>



--
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.casteblanco at gmail.com