Re: ABF with the RMSD colvar

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Apr 16 2014 - 13:41:54 CDT

Hi George, if you want to drive the system from A to B in a monotonic way
as you suggest, you should probably define a moving harmonic potential that
goes between the RMSD value at A and B.

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.

Giacomo

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
>
>
>
>
>

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