[gmx-users] Contribution of delta bonding energy in the delta free energy

[Justin A. Lemkul]

afsaneh maleki wrote:
> Dear Mark,
>  
> I used thermodynamics integration method (TI) to obtain delta Gibbs 
> energy of the protein membrane with dual topology.
> 
> topology A (lambda=0) to topology B (lambda=1)
> 

What did you alter between these two topologies?  Nonbonded terms (atom types 
and/or charges)?

> What i obtained after using mdrun command to calculate free energy is 
> dgdl.xvg that contain dV(total)/dlamda via time. I want to obtein 
> dV(bond)/dlamda and dV(non-bond)/dlamda, seperetly. dV(bond)/dlambda and 
> dV(non-bond)/dlambda are not writed in free.edr and free.log. how to 
> produce dv(bond)/dlambda and dV(non-bond)/dlambda.
> my version gromacs is 4.0.5 and 4.0.7.
>  

If you simply removed/added charges and/or van der Waals terms, then 
dV(bonded)/dlambda = 0 since the bonds are unaffected.  If you are looking to 
completely remove all bonded and nonbonded terms from a given molecule, you will 
have to do extensive topology modifications to eliminate bonds, but in that case 
your molecule will just fly apart (as a function of lambda) and give a 
meaningless result.  You can mutate molecules (e.g. FEP of molecule A to B), but 
completely turning off all intra- and inter-molecular interactions using TI does 
not lend well to obtaining the information you seek.

-Justin

>  
> Thanks in advance,
> Maleki
> 
> On Tue, Aug 9, 2011 at 6:18 AM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
> 
>     On 9/08/2011 9:13 PM, afsaneh maleki wrote:
>>
>>     Hi,
>>
>>      
>>
>>     I used thermodynamics integration method (TI) to obtain delta
>>     Gibbs energy of the protein membrane. I want to separate
>>     contributions of delta bonding and nonbonding energy in delta
>>     Gibbs energy.
>>
> 
>     So instead of using the sum of bonded and non-bonded energy (i.e.
>     total PE), use them separately. Whether that will mean anything is
>     up to you to demonstrate.
> 
>     Mark
> 
>>      
>>
>>     Best wishes,
>>
>>     Maleki,
>>
>>
>>
> 
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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