From: Michelle Kuttel (mkuttel_at_cs.uct.ac.za)
Date: Wed Nov 23 2011 - 14:03:22 CST
Hi all
On 23 Nov 2011, at 6:41 PM, Jérôme Hénin wrote:
> Hi guys,
>
> On 23 November 2011 16:28, Giacomo Fiorin <giacomo.fiorin_at_gmail.com> wrote:
>> Hi Michelle. What you describe seems to me that the angle gets stuck into a
>> local minimum. This is pretty typical when you minimize. Then when you try
>> the next window, you don't get the results you want because your angle is
>> stuck.
>>
>> I would start all windows from the same initial structure and change the
>> center of the static restraint, rather than changing it on the fly while you
>> minimize. That would be most appropriate for dynamics.
>
> I am not sure that will work so well. The problem is more fundamental:
> if the potential is corrugated enough that you get stuck in local
> minima, then the relaxed scan is always tricky. I run into this once,
> and one test I did was to run the scan both ways to see if I sampled
> the same conformations - and if not, which one had lower energy.
>
> You could try scanning this angle while doing MD, to give the molecule
> a chance to optimize itself beyond the nearest local minima.
>
> Once the "true" minima are identified, you might have to run the scan
> in pieces, starting from the properly minimized structures and
> sampling the barriers around going both ways. In the worst case, the
> landscape is too complex to be sampled like this, then you'd need some
> kind of MC search rather than just a torsional scan.
Actually, this is a very simple dihedral angle in a very small molecule: the primary alcohol in glucose. I was running it as a test, to validate the force field in NAMD (it's a CHARMM ff) and procedure before I continue with more complex calculations. It really is one of the simplest cases you can get, so colvars with "harmonic" *should* work for calculating a relaxed map. BTW, the ABF routine works beautifully on the same dihedral, so I think that I am forced to conclude that "harmonic" does not actually work for calculating relaxation maps. Or at least not reliably.
>
>
>
>> On Wed, Nov 23, 2011 at 9:16 AM, Michelle Kuttel <mkuttel_at_cs.uct.ac.za>
>> wrote:
>>>
>>> The plot thickens....
>>> After much experimenting, I have finally determined that, for this
>>> particular dihedral, the optimal "harmonic" configuration is:
>>> harmonic {
>>> name scanOmega
>>> colvars Omega
>>> centers -180
>>> targetCenters 180
>>> targetNumSteps 500 #these
>>> targetNumStages 72 #are the values
>>> forceConstant 0.005 # in question
>>> }
>>> So ,it seems that my previous values were far too "high". However, I
>>> still don't understand why, if I increase targetNumStages and
>>> targetNumSteps, I need to increase the force constant as well.
>>> "targetNumSteps" should just be number of minimization steps at a
>>> particular force, surely, and not affect the applied force, right? But it
>>> does!
>
> Note that the force constant is in unit of kcal/mol/square colvar
> unit, where the effective colvar unit is given by the width parameter.
> Here, it is 0.5 degrees, which is very small, meaning that a force
> constant of 100 is really huge (deviating from the restraint center by
> 0.5 degrees costs 100 kcal/mol of energy). A looser restraint leaves
> more leeway for various degrees of freedom to relax, possibly yielding
> a better optimization.
>
> The reason targetNumStages matters is, you may not get trapped in the
> same local minima depending on the size of the "hops" in the reference
> torsional angle.
But this is a simple dihedral, with only three minima (at -60, 60 and 180 degrees) - and these minima are not where it gets stuck....
I am still not clear on why "targetNumSteps" affects the force....?
Many thanks
Michelle
>
> Best,
> Jerome
>
>>> The use of "harmonic" to create relaxed energy maps is not documented in
>>> the NAMD User Guide, other than the comment:
>>> "The harmonic biasing method may be used to enforce fixed or moving
>>> restraints, including variants of Steered and Targeted MD. Within energy
>>> minimization runs, it allows for restrained minimization, e.g. to calculate
>>> relaxed potential energy surfaces.".
>>> So, I would really appreciate it if someone can explain this to me.
>>> Pretty please?
>>> Michelle
>>>
>>> On 21 Nov 2011, at 12:45 PM, Michelle Kuttel wrote:
>>>
>>> Hello
>>> I am trying to calculate a simple relaxed energy profile for a dihedral
>>> angle (this is a simple sanity check - I can compare the profile to one I
>>> calculated some time ago in CHARMM).
>>> I am using colvars and harmonic restraints to do this. My colvarsConfig
>>> file looks like this:
>>> ------------------------------------
>>> colvarsTrajFrequency 10000
>>> colvar {
>>> name Omega
>>> width 0.5
>>> dihedral {
>>> group1 {
>>> atomnumbers { 7 }
>>> }
>>> group2 {
>>> atomnumbers { 5 }
>>> }
>>> group3 {
>>> atomnumbers { 20 }
>>> }
>>> group4 {
>>> atomnumbers { 21 }
>>> }
>>> }
>>>
>>> }
>>> harmonic {
>>> name scanOmega
>>> colvars Omega
>>> centers -180
>>> targetCenters 180
>>> targetNumSteps 10000
>>> targetNumStages 36
>>> forceConstant 100
>>> }
>>> ----------------------------
>>> In my main file, I then have the line:
>>> minimize 370000
>>> This works OK (though the energies for the first few stages are a bit
>>> high). HOWEVER, when I change "targetNumStages 36" to "targetNumStages 72"
>>> and "minimize 370000" to "minimize 730000", suddenly I need a much higher
>>> force of 200 for it to work. If I don't increase the force, the omega angle
>>> (recorded in the .traj file) "stalls" at -145 degrees. The angle does not
>>> rotate further than this on subsequent stages.
>>> Why would increasing the number of stages require a higher force? I
>>> thought that the width of the omega colvar would still be the same (0.5
>>> degrees) and therefore the scaling should be the same?
>>> I think that I do not understand the way forces are applied under harmonic
>>> restraints and I would really appreciate some insight!
>>> Many thanks
>>> Michelle
>>> ---------------------------------------------
>>> Dr Michelle Kuttel
>>> Department of Computer Science
>>> University of Cape Town
>>> Cape Town
>>> South Africa
>>> mkuttel_at_cs.uct.ac.za
>>> PH: +27 21 6505107
>>> ---------------------------------------------
>>>
>>>
>>>
>>
>>
>
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