[gmx-users] Re: Re: T->A mutation for a dimer protein

[Lishan Yao]

On 23/06/2011 12:22 PM, Lishan Yao wrote:
> Dear Chris and Mark,
>      Thank you both for the response. I did the simulation already and Gromacs only gives me the total dH/dl.

So what's wrong with dividing by two, like I suggested last time? You've 
got two events and you assert that they're independent, so the 
statistics should be easy.
---
I want an error estimation of the free energy change. not sure how if I only know the sum of the two.

>   The two mutated sites are more than 20A alway from each other which makes it safe to assume that the interaction between the two sites is small. If I can extract dH/dl for each site, I could get a resonable error estimation of my calculation. Furthermore, if this is reliable I will do different mutations in two monomers (as long as they are away from each other) so that I can save my computational time by 50%. I guess this will involve some code change.

To which mutation would you assign the energy contribution of the atoms 
around half way between them?
---
I do not intend to assign energy contribution to each surrounding atom.  Gromacs gives dH/dl = dH/dl (monomer 1 site) + dH/dl (monomer 2 site). My question is whether it is possible to extract dH/dl (monomer 1 site) and dH/dl (monomer 2 site) separately. I would think it should be straightforward practically.

Best,
Lishan



Mark

> Best,
> Lishan
>