On 23/06/2011 7:59 PM, Lishan Yao wrote:
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.
If I say the sum of the heights of n independent people is x with
estimated error of y, you have useful information about the height of a
single independent person, and its error estimate. Details vary with the
details.
Mark
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
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
