From: George Patargias (gpat_at_bioacademy.gr)
Date: Mon May 19 2014 - 05:01:12 CDT
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
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