[gmx-users] Re: forward and reverse free energy not consistant (Li Qiang)

[Gerrit Groenhof]

Looks like hysteresis. Do you do slow growth, or discrete FEP?

Gerrit



> Dear all Gmxers,
>
> I am calculating a mutation free energy from L<->A for a five AA 
> peptides using G96 53a6 force field.
> however, my dG_for and dG_rev is quite different.
> dG_for(lambda=0.00) = - 9.9 kJ/mol
> dG_rev(lambda=1.00) =   1.33 kJ/mol
>
> Is there anything wrong with setting up topologies?
>
> Here is the [atoms] part for morphed atoms. and I attached the full .top 
> in the attachment.
> For L->A:
> [ atoms ]
>     17        CH2      2    LEU     CB      6          0     14.027      
> CH3   0   15.035; qtot 1
>     18        CH1      2    LEU     CG      7          0     13.019      
> DUM   0   13.019; qtot 1
>     19        CH3      2    LEU    CD1      7          0     15.035      
> DUM   0   15.035; qtot 1
>     20        CH3      2    LEU    CD2      7          0     15.035      
> DUM   0   15.035; qtot 1
>
>
> For A->L :
> [ atoms ]
>     17        CH3      2    ALA     CB      6          0     15.035      
> CH2    0    14.027; qtot 1
>     60        DUM      6    DUM    DUM     24          0    13.019      
> CH1    0    13.019
>     61        DUM      6    DUM    DUM     24          0    15.035      
> CH3    0    15.035
>     62        DUM      6    DUM    DUM     24          0    15.035      
> CH3    0    15.035
>
> thanks for help
>
> LQ
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