Re: ABF: moving system in Z direction

From: Giacomo Fiorin (
Date: Mon Apr 19 2010 - 12:16:08 CDT

Hi Sefer

1. and 2. Movements in all directions (x, y and z) won't be a problem,
because the distanceZ component is calculated with PBC taken into account.
Just make sure you didn't specify 'wrapAll' in the case of a multimeric
channel. We wrote this in the user guide, but it doesn't hurt to remind it.

3. The theoretical range goes from -l_z/2 to l_z/2, unless you put in some
walls to confine the ammonium. If you haven't seen negative values yet, it
may be simply that you haven't sampled that region yet, but that you will
later in the simulation. But, if the minimum value is *exactly* zero, there
is something strange going on. What are your lowerBoundary and
upperBoundary? They should be a negative number and a positive number, for

4. I believe it's correct. SHAKE forces that constrain the bond length do
affect the forces that ABF is sampling. But this contribution will cancel
out if you also include all the other atoms that are involved in the
constraint, *and* provided that what enters the definition of the colvar is
the position of the center of mass (in this case, of the ammonium). All the
distance-like components do make use of the center of mass only.


---- ----
Giacomo Fiorin
  ICMS - Institute for Computational Molecular Science
    Temple University
    1900 N 12 th Street, Philadelphia, PA 19122
---- ----

On Mon, Apr 19, 2010 at 9:49 AM, sefer baday <> wrote:

> Hello,
> 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.
> Thanks
> Sefer Baday
> University of Basel

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