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

[Li Qiang]

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
-------------- next part --------------
A non-text attachment was scrubbed...
Name: topol_A2L.top
Type: application/x-extension-top
Size: 15230 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080616/562fa99f/attachment.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: topol_L2A.top
Type: application/x-extension-top
Size: 15189 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080616/562fa99f/attachment-0001.bin>