Re: ABF: moving system in Z direction

From: Jérôme Hénin (
Date: Mon Apr 19 2010 - 11:20:35 CDT

Hi Sefer,

On 19 April 2010 15:49, 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 ?

Not if the reaction coordinate is defined in a sensible way, i.e.
reflects the position of the ion with respect to the pore.

> 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.

Do you mean you get different _converged_ values? The comparison after
a short time might not be very informative.

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

Hard to tell without more information... Unless the motion seems
artefactual (e.g. far from equilibrium), it should be fine.

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

This is normal and purely conventional anyway. This has been discussed
on the list recently.

> 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.

This is correct.

> Thanks

No problem. Please say hi to Simon for me.


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