From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Apr 25 2014 - 09:41:54 CDT
> Basically, if I understood correctly, what are you suggesting here is to
> do targeted/steered MD using the RMSD colvar as mentioned in Usage case 5
> in your paper "Using collective variables to drive molecular dynamics
> simulations"
>
> I saw in the colvars manual that the PMF can be extracted from the colvars
> trajectory file (having switched on outputAccumulatedWork flag) but I am
> not quite sure how to do this: by averaging somehow the accumulated work
> curve?
>
>
The averaging of the ensemble of states of a single simulation is done by
using the accumulated work flag itself (forces working in favor of the
transformation or against it will be averaged simply by integrating both).
To average between multiple simulations, use the well known Jarzynski's
formula.
> > ABF will try to iteratively calculate the free energy profile, but the
> precise trajectory between A and B cannot be predicted. Use it to quantify
> > the free energy change, i.e. when you know that you can use a MD
> simulation
> > with enough length to sample the ensemble of states.
>
> Are you saying here that the *same* RMSD colvar definition used for the
> targeted/steered MD (and described in my previous email) together with
> "abf" bias (instead of "harmonic") is not going to generate a reliable
> PMF?
>
You can define the same exact colvar but apply different methods to it and
thus obtain different results, which should be equivalent in the limit of
very long simulation time.
You mentioned a 7-subunits protein, i.e. a very complex system, for which
you should anticipate that to obtain a reliable PMF won't be easy. Doing
preliminary tests such as a steered MD (aka a targeted MD in this case) to
get an idea of the transformation pathway can be a good idea. Then when
you know a bit about the transformation, use whichever free energy
calculation method you think most appropriate.
Giacomo
>
> Best wishes
> George
>
>
>
> > On Wed, Apr 16, 2014 at 6:14 AM, George Patargias
> > <gpat_at_bioacademy.gr>wrote:
> >> Hi Giacomo,
> >> Sorry for the hassle; just one more question on this particular ABF
> calculation.
> >> If I want to study the conformational transition A --> B and use the
> structure of B as a reference for the RMSD colvar, is the ABF bias going
> to "drive" the RMSD of A with respect to B from the upperboundary value
> (that I will calculate by superimposing A and B) to the
> >> lowerboundary
> >> value (a small one, like 0.1)?
> >> George
> >> > Yes, avoid using wrapAll in this case. Non covalently linked protein
> >> fragments would be wrapped individually, and mess up the calculation of
> the
> >> > RMSD.
> >> > Giacomo
> >> > On Tue, Apr 15, 2014 at 6:22 AM, George Patargias
> >> > <gpat_at_bioacademy.gr>wrote:
> >> >> Hello,
> >> >> I am trying to set up an ABF calculation using the RMSD colvar. The
> >> atom
> >> >> block of the colvar configuration file contains all the C-alpha
> atoms
> >> of
> >> >> a
> >> >> protein complex that consists of 7 (non covalently linked) subunits.
> >> I
> >> am trying to decide whether I need to exclude the wrapAll option (and
> use only wrapWater) on the basis of the recommendations found here
>
> http://www.ks.uiuc.edu/Research/namd/2.9/ug/node55.html#SECTION000132410000000000000
> I would really appreciate any tips on this
> >> >> Thanks!
> >> >> Dr. George Patargias
> >> >> Postdoctoral Research Fellow
> >> >> Biomedical Research Foundation
> >> >> Academy of Athens
> >> >> 4, Soranou Ephessiou
> >> >> 115 27
> >> >> Athens
> >> >> Greece
> >> >> Office: +302106597568
> >> Dr. George Patargias
> >> Postdoctoral Research Fellow
> >> Biomedical Research Foundation
> >> Academy of Athens
> >> 4, Soranou Ephessiou
> >> 115 27
> >> Athens
> >> Greece
> >> Office: +302106597568
>
>
> Dr. George Patargias
> Postdoctoral Research Fellow
> Biomedical Research Foundation
> Academy of Athens
> 4, Soranou Ephessiou
> 115 27
> Athens
> Greece
>
> Office: +302106597568
>
>
>
>
>
>
>
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