**From:** George Patargias (*gpat_at_bioacademy.gr*)

**Date:** Mon May 19 2014 - 05:01:12 CDT

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Hello Giacomo,

Thanks again for these very useful comments.

I am trying to select a proper value for the force constant of the moving

restraint that will act on the RMSD colvar. A value of 10. kcal/mol/A^2

(that you mention in http://colvars.github.io/) seems to be quite small

for a protein with 1980 C-alpha atoms (like in my case); i.e. the force

acting on each C-alpha turns out to be very small (10/1980)

On the other hand, in the TMD section of the NAMD 2.9 manual it is

mentioned that a value of 200 kcal/mol/A^2 "seems to work well in many

cases". But there, this K is in equation U = 0.5*K/N*(RMS(t)-RMS*(t))^2

where N is the number of targeted atoms.

Does it make sense to select a forceConstant of c.a 1000 kcal/mol/A^2 that

will come down as ~0.5 kcal/mol/A^2 for each atom?

Concerning the centers flag, I determined its value by super-imposing the

current with the reference coordinates and calculating the RMSD. Is this

correct?

Best wishes

George

*> 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
*

Dr. George Patargias

Postdoctoral Research Fellow

Biomedical Research Foundation

Academy of Athens

4, Soranou Ephessiou

115 27

Athens

Greece

Office: +302106597568

**Next message:**Lorenz Ripka: "COLVAR metadynamics: center of mass of atoms crossing simulation box"**Previous message:**David Brandon: "Workshop on Very Large System Simulation Workshop, Urbana, IL, August 11-15, 2014"**Next in thread:**Giacomo Fiorin: "Re: Steered MD with the RMSD colvar"**Reply:**Giacomo Fiorin: "Re: Steered MD with the RMSD colvar"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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