[gmx-users] Free Energy Calculations

[Live King]

Hi Everyone,
I use ancient version of Gromacs 4.5.5 for free energy calculations. I have
two different questions.

1) When I run g_bar for results, I get this

lambda  0.000 -  0.050,   DG -2.16 +/-  0.00
lambda  0.050 -  0.100,   DG -2.16 +/-  0.01
lambda  0.100 -  0.150,   DG -2.09 +/-  0.01
lambda  0.150 -  0.200,   DG -1.98 +/-  0.01
lambda  0.200 -  0.250,   DG -1.83 +/-  0.01
lambda  0.250 -  0.300,   DG -1.59 +/-  0.00
lambda  0.300 -  0.350,   DG -1.26 +/-  0.00
lambda  0.350 -  0.400,   DG -0.80 +/-  0.00
lambda  0.400 -  0.450,   DG -0.17 +/-  0.00
lambda  0.450 -  0.500,   DG  0.67 +/-  0.00
lambda  0.500 -  0.550,   DG  1.79 +/-  0.00
lambda  0.550 -  0.600,   DG  3.30 +/-  0.01
lambda  0.600 -  0.650,   DG  4.35 +/-  0.11
lambda  0.650 -  0.700,   DG  1.99 +/-  0.10
lambda  0.700 -  0.750,   DG  0.61 +/-  0.04
lambda  0.750 -  0.800,   DG  0.04 +/-  0.02
lambda  0.800 -  0.850,   DG -0.44 +/-  0.04
lambda  0.850 -  0.900,   DG -0.46 +/-  0.02
lambda  0.900 -  0.950,   DG -0.43 +/-  0.04
lambda  0.950 -  1.000,   DG -0.49 +/-  0.02

total   0.000 -  1.000,   DG -3.13 +/-  0.21


Where these results are stored. I don't seem to find them anywhere.
Barint.xvg seems to contain something else. Please let me know if they get
stored or not and If they don't please let me know how to store it ? ( of
course without copy and pasting into the text file).


2) The results I showed above always show this warning :-




*"WARNING: Some of these results violate the Second Law of Thermodynamics:
         This is can be the result of severe undersampling, or (more
likely)         there is something wrong with the simulations".*

I have checked for both possible suggestions.I don't seem to find anything
wrong with my simulations. Sometimes this warning goes away if I increase
the time span. But, most of the times it keeps coming back. What does that
mean ? How can I get rid of that ?


Thanks,
Vikas