[gmx-users] Irregular relative entropy in free energy calculation

[Mark Abraham]

Hi,

Clearly something is garbage about that last simulation, but you won't know
why until you start looking at it output. :-) Just guessing that the table
is wrong won't help you. Make a trivial system that you can use to prove
your table is right ;-)

Mark

On Mon, 17 Jul 2017 19:54 Patrick armstrong <patricarm16 at gmail.com> wrote:

> Hi all,
>    I am calculating the solvation energy of a LJ system, where one bead is
> solvated in 1200 beads in a box. There is only LJ interaction between beads
> and the interactions between beads are all the same. I calculated the free
> energy with BAR method. For LJ 12-6 interaction it works well. While when
> the LJ 9-6 interaction  was applied it showed irregular values for the
> relative entropy as below.
>
>   lam_A  lam_B      DG   +/-     s_A   +/-     s_B   +/-   stdev   +/-
>      0      1   -0.17  0.00    0.00  0.00   -0.00  0.00    0.01  0.00
>      1      2   -0.19  0.00   -0.00  0.00   -0.00  0.00    0.01  0.00
>      2      3   -0.20  0.00    0.00  0.00    0.00  0.00    0.01  0.00
>      3      4   -0.22  0.00    0.00  0.00    0.00  0.00    0.01  0.00
>      4      5   -0.25  0.00   -0.00  0.00   -0.00  0.00    0.01  0.00
>      5      6   -0.29  0.00   -0.00  0.00    0.00  0.00    0.01  0.00
>      6      7   -0.35  0.00   -0.00  0.00    0.00  0.00    0.01  0.00
>      7      8   -0.46  0.00   -0.00  0.00    0.00  0.00    0.02  0.00
>      8      9   -0.74  0.00    0.00  0.00    0.00  0.00    0.04  0.00
>      9     10   -1.12  0.03 26835097.52 1029204.76    3.58  0.03    6.34
> 0.09
>
> I think maybe it is due to the tabulated potential. Did anyone have similar
> problem previously? The GMX version is 5.1.2. Thanks in advance,
>
> Patrick
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