[gmx-users] hydration free energy

[asaffarhi at post.tau.ac.il]

Hi,

Do you know which values of lambdas are used?
Are you using a soft-core technique?

Asaf

Quoting dgfd dgdfg <roinato at mail.ru>:

> Hi. I have calculated deltaG of hydration for my molecule in 101  
> steps. First 50 steps I decoupled coulomb interactions and last 50 -  
> vdw. After all I calculated resulting value by the command
> gmx bar -f {0..100}/dhdl.xvg -o -oi -oh -b 500 >RESULT
> and found such phrase in the output
>
> Temperature: 300 K
> Detailed results in kT (see help for explanation):
>  lam_A  lam_B      DG   +/-     s_A   +/-     s_B   +/-   stdev   +/-
>      0      1    8.16  0.11    0.34  0.06    0.34  0.06    0.91  0.02
>      1      2    7.61  0.07    0.21  0.08    0.19  0.07    0.86  0.01
> ...
> ...
> ...
>     97     98   -0.40  0.02    0.42  0.02    0.55  0.02    0.97  0.01
>     98     99   -2.11  0.03    1.16  0.03    1.84  0.06    1.75  0.03
>     99    100  -17.55  0.43   13.60  0.44 62204236256674537472.00  
> 33302891096617504768.00  102.60 10.21
> 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.
>
> Please answer what is wrong in my simple algorythm. It is based on  
> tutorial   
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html with some simplification. All necessary data  
> attached.
>
> ----------------------------------------------------------------------