Fine :)
So forget what I wrote before...I mentioned exactly that :)
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/
[EMAIL PROTECTED] wrote:
Hi maik
I made the calculation with sc-power=2 adding 3 lambda values. Now i get
integrating the plot of average free energy for the mutation of toluene in
water 0.559 instead of 15,8 in previous calculation.
if i combine with the free energy in vacuo i have -3,41 KJ/mol vs (-3,1
KJ/mol exp.). This is quite ok!!!!!! :)
So the error was a combination of number of points- sc-parameter but for
sure number of points are really important for the integration part!!! in
the calculation of free energy.
. regards
geraldine
On Fri, February 15, 2008 11:07 am, Maik Goette wrote:
I had a veeery short look into the tutorial and found an error.
DG_hyd=DG_1-DG_3-DG_2 for the cycle is wrong.
The correct cycle would be:
DG_1+DG_3=DG_hyd+DG_2
=>DG_hyd=DG_1-DG_2+DG_3 with DG_3 =0
So its:
DG_hyd=DG_1-DG_2 instead of DG_hyd=DG_1-DG_3
Anyway, this won't help you, cause the only effect is a change of the
sign to +19 and therefore worse.
Can you show me the topology, you made?
As far as the free energy experts here discussed it, sc-power=2
shouldn't be the lambda-dependance of choice. I can agree to that from my
simulations.
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/
[EMAIL PROTECTED] wrote:
Hi maik
the energy DEltaG_hyd=deltaG_mutation(vacuo)-deltaGmutation(water)
for fisrt one deltaG_mutation(vacuo) =-2,85 for second
deltaGmutation(water) =15,87
so i found DEltaG_hyd = -19 kj/mol instead of -3,1 kj/mol
i'll do a series of calculation with sc-power=2 and see the difference
see if there's some significant difference. geraldine
On Thu, February 14, 2008 10:57 am, Maik Goette wrote:
Hi
Now, make sure, that you apply the thermodynamic cycle correctly.
I wouldn't wonder about large errors. Depending on the definition of
large. Error estimation from free energy calculations can be very
tricky. Using mpi shouldn't influence your calculations outcome.
Still I don't know the error.
How to post the numbers: Exp. value (+error) and your calculated value
(+error) ? From those I could tell you if something is terribly
wrong or not. :)
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/
[EMAIL PROTECTED] wrote:
Hi MaiK,
Sorry i forgot the subject. Thank you to have answered this email.
This
tutorial is about solvation free energy of toluene using
thermodynamical cycles. two energies have to be calculated according
to this cycle, the hydration energy of toluene and the mutation
energy from dummy to toluene in vacuo. For each energy calculation
several MD simulation for different lambda value must be performed.
in the mdp files given i added the line sc-power=1 and made the
calculation. from the file dgdl.xvg obtained for each lambda value i
used the g_analyse command to get the average and the estimated
error of free energy. i made the plot <dgdl>=f(lambda) for the first
part (hydration of toluene) integrated and get the integrated value
of the plot and did the same for mutation energy of toluene and made
the difference of the two integrated values. I really don't know
where the error came from : -version of gromacs, the fact that mpi
has been used for the first part and single process for the mutation
part (because of shake block problem) won't change anything i guess,
I would carefully go through one
more time and check why i didn't get the right value. I don't know
if this high estimated error is really problematic. regards
geraldine
On Wed, February 13, 2008 6:19 pm, Maik Goette wrote:
Hi
First of all: You can be quite happy, if anyone reads a "no
subject" mail. sc-power seems to be set to zero in the newer
version, in contrast to the old ones, where it was 1 by default.
Therefore GROMACS
complains. 1 is the value, you should use. I don't know the
tutorial, but if you use exactly the files given there (and add
sc-power = 1), you should get values, which are close to the
experimental one (I guess, cause a tutorial won't make sense, if
the files don't yield the desired value).
Sorry, but more help is hard to give with so few information.
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/
[EMAIL PROTECTED] wrote:
Hi all,
i 'm a beginner in molecular dynamics. I was doing the tutorial
of md group, hydration free energy of toluene :
http://md.chem.rug.nl/education/Free-Energy_Course/2.hydration-
fe.h tml
i have some problems regarding the calculation of toluene in
water. the thing is that in the examples files equ-10.00.mdp and
data-10.00.mdp no sc-power were mentioned and doing the
calculation the error files mentioned about sc-power must be >0
so i added this line sc-power=1 to those files. Analyzing the
dgdl.xvg files the estimate error(err. est.) is about 5.79....
for each lambda value studied while the mutation of toluene to
dummy in vacuo gave really reasonable rms of about 10E-5.
Combining the integration value of
the plot in water and vacuo did not give me the right solvation
free energy value (compare to experimental one). i assumed that
this is the free calculation in water which is problematic. I
tried to play with sc-power and sc-alpha but still even if those
parameters seem to influence a lot on the energy no real
improvement are visible. Would you have any idea what could be
the problem? geraldine Helsinki university
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