[gmx-users] Re: free energy calculations of methane in water computed by GMX ver 4.5.7 and ver 4.6.2

[Justin Lemkul]

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

-- 
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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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