[gmx-users] forward and reverse free energy not consistant

[Jochen Hub]

Could it be that you get a substantial hysteresis since you do the 
mutation quite fast (non-equilibrium effect, dissipative work, etc.)? 
Check the dgdl file and  maybe increase the simulation time.

cheers, Jochen

Li Qiang wrote:
> 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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-- 
************************************************
Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312
************************************************