From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Fri Dec 17 2010 - 13:22:49 CST
In ABF (NAMD 2.6), I see that the difference between "zCoord" and "zCoord-atom" is that the first one stands for the selection of a single atom of interest while the second one is for a group of atoms of interest. I am having a single ion , moving along the channel so, I have to use "zCoord-1atom". However, I realized that I made a mistake in preparing my configuration file (I used "zCoord" and addressed just one ion for atom selection" and I didn't get any related error during the simulation. Now the simulation is finished. Are the results reliable or I need to repeat that with the right command (zCoord-atom)?
I have another question:
My understanding from zCoord or zCoord-1atom is that we rotate the system to put the channel along Z axis first and The program always takes this as the Z axis during the simulation. Then we define two groups as "the reference atoms" and "the ion of interest", and we also define two boundaries (let's say 7 and 10). Then the program is supposed to move the "ion of interest" along channel "z axis" from "7 A" to "10 A" with respect to the COM of the "reference atoms". Right? However, in my system and I think in all the systems both the "reference atoms" and "the ion of interest" are moving freely so that the distance I defined at the beginning "7 to 10" is not staying the same anymore unless we fix the atoms to stay there or the atoms move really slow. I am wondering If we we don't fix the atoms and let them move freely , how does the program work to move the ion between "7 and 10"? I mean does the program always refer to the very first definition of atom positions and apply the "distance 7 to 10" to this? or somehow, it compensates for this movements so that the area of sampling is still between 7 to 10 as we defined. Or does the program calculate the COM of the reference for each time step and moves the ion with respect to that between "7 and 10"? This way in the case of fast movement if there is no fixed atoms,... there is no guarantee that the sampling area is the same as what we expected. Right?
I apologize if my questions seem naive. I ran my simulation without fixing any atoms and I figured out that in all simulations the whole system is moving which causes the ion not to be along Z axis in some windows anymore. I am still learning this method and would really appreciate if some one could give me some hints in this case
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