On 6/23/13 1:13 AM, Dwey wrote:
Hi Justin,
Thank you for sharing your experience with me.
As suggested, Gromacs ver 4.5.5 is compiled within the same Linux box
and I am able to reproduce a similar result ( DG= -9.30 kJmol-1).
Gromacs ver 4.5.5 and 4.6.2 both are compiled from source codes, while
Gromacs ver 4.5.7 as reported earlier is installed with pre-compiled
binary files.
Thus, Gromacs ver 4.5.7 is now re-compiled again by myself. Below are
shown results.
In addition, L-BFGS mdp file works well for all versions after it is
modified by adding "define = -DFLEXIBLE".
++++++++++++++++++++++++++++++++++++
Gromacs ver 4.5.5 (compiled from source codes)
point 0.050 - 0.100, DG -0.04 +/- 0.00
point 0.100 - 0.150, DG -0.08 +/- 0.00
point 0.150 - 0.200, DG -0.13 +/- 0.01
point 0.200 - 0.250, DG -0.19 +/- 0.00
point 0.250 - 0.300, DG -0.27 +/- 0.00
point 0.300 - 0.350, DG -0.35 +/- 0.00
point 0.350 - 0.400, DG -0.43 +/- 0.01
point 0.400 - 0.450, DG -0.55 +/- 0.01
point 0.450 - 0.500, DG -0.71 +/- 0.01
point 0.500 - 0.550, DG -0.94 +/- 0.00
point 0.550 - 0.600, DG -1.25 +/- 0.00
point 0.600 - 0.650, DG -1.40 +/- 0.01
point 0.650 - 0.700, DG -1.29 +/- 0.01
point 0.700 - 0.750, DG -1.01 +/- 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 0.050 - 1.000, DG -9.30 +/- 0.03
++++++++++++++++++++++++++++++++++++
Gromacs ver 4.5.7 (compiled from source codes)
lambda 0.000 - 0.050, DG 0.05 +/- 0.00
lambda 0.050 - 0.100, DG 0.02 +/- 0.00
lambda 0.100 - 0.150, DG -0.04 +/- 0.00
lambda 0.150 - 0.200, DG -0.09 +/- 0.00
lambda 0.200 - 0.250, DG -0.14 +/- 0.01
lambda 0.250 - 0.300, DG -0.21 +/- 0.01
lambda 0.300 - 0.350, DG -0.29 +/- 0.01
lambda 0.350 - 0.400, DG -0.37 +/- 0.00
lambda 0.400 - 0.450, DG -0.48 +/- 0.01
lambda 0.450 - 0.500, DG -0.65 +/- 0.01
lambda 0.500 - 0.550, DG -0.89 +/- 0.01
lambda 0.550 - 0.600, DG -1.19 +/- 0.01
lambda 0.600 - 0.650, DG -1.34 +/- 0.01
lambda 0.650 - 0.700, DG -1.23 +/- 0.00
lambda 0.700 - 0.750, DG -0.95 +/- 0.01
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 0.19 +/- 0.00
lambda 0.950 - 1.000, DG 0.38 +/- 0.00
total 0.000 - 1.000, DG -8.19 +/- 0.03
++++++++++++++++++++++++++++++++++++
After comparing the output from ver 4.5.5 with that from ver 4.5.7, I
do find quirky information from the g_bar in ver 4.5.7.
In ver 4.5.7, for example, it shows that ver 4.5.7 dose not give
information of dH/dl (see below)
Moreover, I also try g_bar of ver 4.5.5 or 4.6.2 to process the output
data (such as md*.xvg generated by ver 4.5.7). The result is
unchanged and DG ( -8.19 kJmol-1) remains incorrect.
Thanks,
Dwey
++++++++++++++++++++++++++++++++++++++++++++++++++++++
g_bar ver 4.5.7,
md0.05.xvg: 0.0 - 5000.0; lambda = 0.050
foreign lambdas: 0.050 (250001 pts) 0.000 (250001 pts) 0.100 (250001 pts)
md0.15.xvg: 0.0 - 5000.0; lambda = 0.150
foreign lambdas: 0.150 (250001 pts) 0.100 (250001 pts) 0.200 (250001 pts)
md0.1.xvg: 0.0 - 5000.0; lambda = 0.100
foreign lambdas: 0.100 (250001 pts) 0.050 (250001 pts) 0.150 (250001 pts)
.
.
.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++
g_bar ver 4.5.5 or 4.6.2,
md0.05.xvg: 0.0 - 5000.0; lambda = 0.05
dH/dl & foreign lambdas:
dH/dl (250001 pts)
delta H to 0 (250001 pts)
delta H to 0.1 (250001 pts)
md0.15.xvg: 0.0 - 5000.0; lambda = 0.15
dH/dl & foreign lambdas:
dH/dl (250001 pts)
delta H to 0.1 (250001 pts)
delta H to 0.2 (250001 pts)
md0.1.xvg: 0.0 - 5000.0; lambda = 0.1
dH/dl & foreign lambdas:
dH/dl (250001 pts)
delta H to 0.05 (250001 pts)
delta H to 0.15 (250001 pts)
.
.
.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Thanks for the detailed information. Please file a bug report on
redmine.gromacs.org with all of this information. We had intended for 4.5.7 to
be the final version in the 4.5.x series, but if there are serious issues with
it, they should probably be corrected.
-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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