Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein

From: Ajasja Ljubetič (
Date: Wed Dec 15 2010 - 10:34:43 CST

Dear Jrme,

>Interesting that you should ask now.
This is great :)
I have just a few questions about the input script.

harmonic {
 colvars chi
 centers -70
 targetCenters 290
 targetNumSteps 10000
 targetNumStages 36
 forceConstant 0.5

In the NAMD input, do I have to specify "minimize 3600000"? And for normal
SMD "run 3600000"?
Will this really preform a full turn or just from -70 to 290 degree?
It currently says in the manual:
"if a complete 360*[image: $ ^{\circ}$]* turn of a dihedral is desired,
multiple runs (at least two) with different targets should be used."

>You are also assuming that the change in average energy is mirrored by
>the change in minimum energy.

Yes, I forgot about that. So in theory running the ABF scan at different
temperatures could be used to get the entropic contribution?

>If I were you, I would start playing around with 2d surfaces and see
>what can be resolved. Of course, the major question is what
>information exactly you want to extract from these simulations.

I would like to see if the lipids influence the conformational space of the
label (and also in what way, ie what is the difference in dihedral angle
distributions). I will first try to find a suitable 2D surface as this
should also be much quicker to calculate.

I have another (unrelated) question that has been bugging me.
Do you (or anybody reading this) happen to know which compiler is used for
the official (windows) NAMD binaries?
While playing with a simple program (just calculates a mandelbrot fractal) I
found that the intel compiler (v10) preforms about 7 times better than MinGW
(GCC) and about 3 times better than Visual studio 2009. The increase
probably comes from the using the SSE3 extensions.
Did anyone play around with compilers and NAMD?

Best regards,

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