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

[friendli]

Hi,

I use thermodynamics integration. 
The protocol is 1000step energy minimization, 20 ps bond-constraint MD, 
and then 200ps MD for collecting dgdl.

thanks

Qiang

Gerrit Groenhof wrote:
> 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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>>
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