ABF: moving system in Z direction

From: sefer baday (SEFER.BADAY_at_unibas.ch)
Date: Mon Apr 19 2010 - 08:49:09 CDT


I work on ion channel. I try to get PMF of ammonium ion moving inside
the pore.
The reaction coordinate is the distance between ammonium ion and
certain residues in the pore, in Z-direction ( distanceZ` option ).
I perform the simulations on namd2.7.

I have few questions about my simulations.

1. In my simulations, protein and lipid complex moves in z-direction.
Does this affect the PMF calculation ?

In order to prevent this I restrained the lipid molecules by applying
SMD constrained. I applied SMD with zero velocity hoping that
center of mass of lipid doesn't move.

SMD on
SMDFile abf_cons_smd.pdb
SMDk 10
SMDVel 0
SMDDir 1.0 1.0 1.0

However, for the different force constants ( for SMD ), I get
different values of PMF.

2. Sometimes, protein also moves in lipid. Does it also have an effect
on ABF ?

3. In my results, the minimum value is always zero, it doesn't become
negative. Is this normal ?

4. I just want to make sure that I am doing the right thing. I apply
ABF for the both hydrogen atoms and nitrogen atom of ammonium molecule.
As far as I understand, if I apply only to nitrogen molecule, bond
between nitrogen and hydrogen might affect ABF.


Sefer Baday
University of Basel

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