[gmx-users] g_bar and second law violations

[Justin Lemkul]

On 11/27/12 11:43 AM, Sanku M wrote:
> Hi,
>    I am trying to compute the free energy change using g_bar: I am using two-stage decoupling process as in Justin Lemkul's tutorial.
> But , I get following warning in all cases regarding violation of second law of thermodynamics. Can someone explain what is this error about and which lambda I should look for?
> Here is the output.
>

You can't have negative entropy.  Several of your simulation windows do, which 
indicates some severe problem, as the error suggests.

-Justin

>   Detailed results in kT (see help for explanation):
>
>   lam_A  lam_B      DG   +/-     s_A   +/-     s_B   +/-   stdev   +/-
>   0.000  0.100   -0.39  0.08   -0.64  0.06   -0.09  0.20    0.88  0.05
>   0.100  0.150    0.08  0.04    0.07  0.03    0.09  0.05    0.43  0.01
>   0.150  0.200    0.12  0.02   -0.11  0.03    0.36  0.06    0.54  0.02
>   0.200  0.300    0.54  0.06   -0.05  0.07    1.25  0.15    1.24  0.03
>   0.300  0.350    0.21  0.03    0.15  0.04    0.31  0.06    0.72  0.01
>   0.350  0.400   -0.01  0.02    0.11  0.03   -0.08  0.04    0.64  0.01
>   0.400  0.500   -0.37  0.03    0.22  0.02   -0.78  0.06    1.07  0.01
>   0.500  0.600   -0.58  0.01    0.17  0.04   -1.17  0.04    0.99  0.01
>   0.600  0.700   -0.74  0.03    0.16  0.02   -1.51  0.07    0.89  0.01
>   0.700  0.750   -0.37  0.01   -0.02  0.02   -0.69  0.03    0.47  0.01
>   0.750  0.800   -0.26  0.01   -0.07  0.01   -0.42  0.02    0.53  0.01
>   0.800  0.850   -0.19  0.01    0.03  0.01   -0.38  0.03    0.57  0.01
>   0.850  0.900   -0.24  0.02    0.06  0.01   -0.50  0.04    0.58  0.01
>   0.900  1.000   -0.47  0.07   -0.04  0.05   -0.12  0.34    1.13  0.06
>
> 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.
>
>
> Final results in kJ/mol:
>
> lambda  0.000 -  0.100,   DG -0.97 +/-  0.19
> lambda  0.100 -  0.150,   DG  0.20 +/-  0.09
> lambda  0.150 -  0.200,   DG  0.30 +/-  0.05
> lambda  0.200 -  0.300,   DG  1.34 +/-  0.15
> lambda  0.300 -  0.350,   DG  0.52 +/-  0.07
> lambda  0.350 -  0.400,   DG -0.02 +/-  0.05
> lambda  0.400 -  0.500,   DG -0.92 +/-  0.08
> lambda  0.500 -  0.600,   DG -1.45 +/-  0.03
> lambda  0.600 -  0.700,   DG -1.86 +/-  0.08
> lambda  0.700 -  0.750,   DG -0.91 +/-  0.03
> lambda  0.750 -  0.800,   DG -0.64 +/-  0.03
> lambda  0.800 -  0.850,   DG -0.48 +/-  0.03
> lambda  0.850 -  0.900,   DG -0.61 +/-  0.04
> lambda  0.900 -  1.000,   DG -1.17 +/-  0.18
>
> total   0.000 -  1.000,   DG -6.68 +/-  0.30
>

-- 
========================================

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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