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

[liqiang]

Hi,

It is 3.3.3. 
are the topology right? Can anybody kindly send me a topology with 
similar mutation so that I can compare?

thanks a lot.

Qiang

Justin A. Lemkul wrote:
> Which GMX version are you using?  There's a known bug in version 3.3.1 
> that has been fixed in 3.3.3.
>
> -Justin
>
> friendli wrote:
>> 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
>>>> -------------- 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://www.gromacs.org/pipermail/gmx-users/attachments/20080616/562fa99f/topol_A2L.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://www.gromacs.org/pipermail/gmx-users/attachments/20080616/562fa99f/topol_L2A.bin 
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> _______________________________________________
>>>> gmx-users mailing list
>>>> gmx-users at gromacs.org
>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at http://www.gromacs.org/search before 
>>>> posting!
>>>>
>>>> End of gmx-users Digest, Vol 50, Issue 50
>>>> *****************************************
>>>>   
>>>
>>> _______________________________________________
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before 
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the www 
>>> interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before 
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www 
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>