Re: ABF: moving system in Z direction

From: sefer baday (
Date: Tue Apr 20 2010 - 04:58:51 CDT

Hi Giacomo,

Thanks for your comments.

On 19 Apr 2010, at 19:16, Giacomo Fiorin wrote:

> 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.

I used wrapAll option. I thought it is fine according to this
criterion " ii) it has all its atoms within the same molecule "
Maybe I misunderstood this one " iv) it is used by a colvar component
that ignores the ill-defined Cartesian components of
its center of mass (such as the x and y components of a membrane’s
center of mass by
distanceZ). "

I will try without wrapALL option.

> 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 distanceZ.

With the zero minimum, I mentioned the value of the PMF. The reaction
coordinate is the distance between pore and the ammonium in Z-
direction. The reaction coordinate is sampled good enough. The
upperBoundary and lowerBoundary is both negative. For my purpose it
doesn't make sense to put like -l_z/2 to l_z/2.

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