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.
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?
Mark
Best,
Lishan
From: chris.ne...@utoronto.ca
Subject: [gmx-users] T->A mutation for a dimer protein
To: gmx-users@gromacs.org
Message-ID:<20110622210442.mmbm5utlww08k...@webmail.utoronto.ca>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
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Dear Lishan:
First, it would be great to see some evidence that you have tried to
do this yourself before posting. Your "I think" makes it a possible
waste of time for us to suggest a resolution to a problem that may or
may not exist.
Second, if indeed it is a problem, perhaps you could use two identical
topologies with different molecule names and treat them separately.
Chris
Message: 3
Date: Thu, 23 Jun 2011 11:40:20 +1000
From: Mark Abraham<mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] T->A mutation for a dimer protein
To: Discussion list for GROMACS users<gmx-users@gromacs.org>
Message-ID:<4e029984.9040...@anu.edu.au>
Content-Type: text/plain; charset="iso-8859-1"
On 23/06/2011 9:48 AM, yaoli...@msu.edu wrote:
Hi All,
I have a protein dimer and I want to calculate a T to A mutation free
energy change using TI method. Since it is a dimer, it is very
convenient (and advantageous) to mutate the T in both monomer
simultaneously. Gromacs will write out dH/dl sum for the two mutations
together, I think. My question is how can I change Gromacs so than
dH/dl for T->A mutation in each monomer is written out separately?
You can't, because both have contributions from all the interactions. If
your method is sound, i.e. both mutations can take place without
affecting the other (big assumption IMO), surely you can just halve
dH/dl from the combined mutation to get the single-mutation dH/dl?
Mark
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