From: George Patargias (gpat_at_bioacademy.gr)
Date: Thu Jul 03 2014 - 06:26:19 CDT
Hello Giacomo,
Thanks for your reply.
I am trying to figure out the meaning of the negative sign in the force
values recorded in the colvars trajectory file.
Is the force on the the RMSD colvar calculated according to the following
equation?
F = k(RMSD(current) - RMSD(target))
where RMSD(target) equals zero since this is the value of the targetCenters
flag.
Best
George
> Hello George, increasing the force constant based on the number of atoms
> is
> a good start, which of course you should check during the simulation.
>
> And obviously, yes, setting the initial center of the restraint potential
> at the RMSD value of the initial configuration is the safest strategy to
> preserve the stability of the system.
>
> Giacomo
>
>
> On Mon, May 19, 2014 at 6:01 AM, George Patargias
> <gpat_at_bioacademy.gr>wrote:
>
>> 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
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
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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