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)
.
.
.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 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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