Re: ABF with the RMSD colvar

From: George Patargias (gpat_at_bioacademy.gr)
Date: Fri Apr 25 2014 - 05:20:31 CDT

Hello Giacomo,

Thanks so much again for these comments.

> 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.

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?

> 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?

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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