On 6/21/13 11:07 AM, Dwey wrote:
Hi gmx-users,
I almost reproduced free energy calculations of methane in water on
Justin's website. First of all, I am able to follow the workflow of
computing solvation free energy for several times with Gromacs version
4.5.7 and version 4.6.2 installed in two identical Linux boxes.
However. the output results of GMX ver 4.5.7 and ver 4.6.2 show different
values of dG
##################################
GMX Ver. 4.5.7:
lambda 0.000 - 0.050, DG 0.05 +/- 0.00
lambda 0.050 - 0.100, DG 0.01 +/- 0.00
lambda 0.100 - 0.150, DG -0.03 +/- 0.01
lambda 0.150 - 0.200, DG -0.08 +/- 0.00
lambda 0.200 - 0.250, DG -0.15 +/- 0.00
lambda 0.250 - 0.300, DG -0.21 +/- 0.01
lambda 0.300 - 0.350, DG -0.28 +/- 0.00
lambda 0.350 - 0.400, DG -0.38 +/- 0.00
lambda 0.400 - 0.450, DG -0.50 +/- 0.01
lambda 0.450 - 0.500, DG -0.66 +/- 0.01
lambda 0.500 - 0.550, DG -0.90 +/- 0.01
lambda 0.550 - 0.600, DG -1.21 +/- 0.01
lambda 0.600 - 0.650, DG -1.37 +/- 0.01
lambda 0.650 - 0.700, DG -1.25 +/- 0.01
lambda 0.700 - 0.750, DG -0.96 +/- 0.00
lambda 0.750 - 0.800, DG -0.62 +/- 0.00
lambda 0.800 - 0.850, DG -0.31 +/- 0.00
lambda 0.850 - 0.900, DG -0.03 +/- 0.00
lambda 0.900 - 0.950, DG 0.20 +/- 0.00
lambda 0.950 - 1.000, DG 0.38 +/- 0.00
total 0.000 - 1.000, DG -8.31 +/- 0.04
##################################
GMX ver. 4.6.2 ver
point 0.000 - 0.050, DG 0.00 +/- 0.00
point 0.050 - 0.100, DG -0.03 +/- 0.00
point 0.100 - 0.150, DG -0.08 +/- 0.00
point 0.150 - 0.200, DG -0.14 +/- 0.00
point 0.200 - 0.250, DG -0.20 +/- 0.00
point 0.250 - 0.300, DG -0.27 +/- 0.00
point 0.300 - 0.350, DG -0.34 +/- 0.00
point 0.350 - 0.400, DG -0.43 +/- 0.01
point 0.400 - 0.450, DG -0.54 +/- 0.01
point 0.450 - 0.500, DG -0.71 +/- 0.01
point 0.500 - 0.550, DG -0.94 +/- 0.01
point 0.550 - 0.600, DG -1.24 +/- 0.02
point 0.600 - 0.650, DG -1.39 +/- 0.02
point 0.650 - 0.700, DG -1.28 +/- 0.01
point 0.700 - 0.750, DG -1.00 +/- 0.00
point 0.750 - 0.800, DG -0.67 +/- 0.00
point 0.800 - 0.850, DG -0.36 +/- 0.00
point 0.850 - 0.900, DG -0.09 +/- 0.00
point 0.900 - 0.950, DG 0.14 +/- 0.00
point 0.950 - 1.000, DG 0.33 +/- 0.00
total 0.000 - 1.000, DG -9.23 +/- 0.03
##################################
The value of DG (= -9.23 kJ mol -1) by GMX ver 4.6.2 is very close to that
by Justin or Shirts et.al of 2.24 kcal mol-1 (~ -9.36 kJ mol -1), while
that of GMX ver 4.5.7 ( =-8.31 kJ mol-1) is far away.
I wonder if someone has similar experience to explain the inconsistency
between the outputs from ver 4.5.7 (~-8.31 kJmol-1) and ver 4.6.2 (-9.23
kJmol-1 ), despite the values of dG computed by others.
I can't explain the difference you are seeing, but I know the results have been
reproduced with versions 4.5.3 and 4.5.5. It is good to know that the latest
version (4.6.2) is working as expected, but it might be useful to figure out
what's up with 4.5.7. Please let me know if you can reproduce the right result
with 4.5.5.
Second, the reason why I almost reproduced dG but not completely is
because I removed the step of L- BFGS minimization. I was not able to
pass this step for both GMX versions. Here shows the warning.
++++++++++++++++++++++++++++
Fatal error:
The combination of constraints and L-BFGS minimization is not implemented.
Either do not use constraints, or use another minimizer (e.g. steepest
descent).
++++++++++++++++++++++++++++
L-BFGS mdp file can be found at
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_l-bfgs.mdp
Add "define = -DFLEXIBLE" to the .mdp file. Water molecules are constrained via
SETTLE, so that causes issues with L-BFGS. When I designed the tutorial, grompp
did not do that check, so it was ignoring those constraints and silently moving
past it. I will fix the .mdp file. Thanks for bringing that to my attention.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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