Re: smd dimer dissociation

From: Jérôme Hénin (
Date: Thu Apr 27 2006 - 12:21:30 CDT

Dear Paweł,

Please see my comments below.

Le Mercredi 26 Avril 2006 21:12, vous avez écrit :
> I have used adaptive biasing force (ABF) method to estimate the change
> of the free energy corresponding to adsorption of a peptide nucleic acid
> (PNA) molecule to a lipid (POPC) - water interface. I equilibrated my
> system for several hundreds of nanoseconds and I see that my PNA
> molecule is attached to the interface. Even more, hydrophobic parts of
> the molecule are a little "immersed" in the non-polar internal part of
> the bilayer. Now, I am trying to pull off the molecule back to the water
> phase to calculate the change of the free energy of the process. Because
> both the PNA molecule and the lipid bilayer are relatively "soft"
> structures, I have used harmonic restraints to avoid their deformation,
> which would of course change the calculated free energy value.

I agree that it would change the free energy value, but which value do you
think is the most physically relevant? My first idea would be that it is the
unrestrained one.
Now, there might be a pracatical issue because a "soft" system also relaxes
more slowly, requiring more simulation time.

> I fixed
> positions of all my N and P1 atoms on one side of the bilayer using the
> constraint "harm" and the force constants fx=fy=fz=50.
There is an issue with these constraints (I am not too happy with that part of
the code, for that matter): you might have read that NAMD usually does not
conserve the total momentum of the system when using PBCs. There are a few
threads on NAMD-L about that. So using restraints with respect to absolute
positions may not have the expected effect.

> I also
> constrained the conformation of the PNA molecule using the constraint
> "dist" between its atoms and the same value of the force constant. My
> simulations run fine as long as they are not canceled, what
> unfortunately occurs at each 10 hours (that is how our allocations are
> technically organized).

Well, I tend to think 24 hours is already not too convenient. 10 hours is
pretty short to run serious calculations.

> When I try to restart I get one of two error
> messages. Usually it is:
> Do you have an idea what I can do to be able to restart my simulations?
> I have also done very similar simulations with another PNA molecule that
> has had no hydrophobic parts (no parts immersed in the organic phase). I
> saw a similar behavior when the molecule was near the interface, but it
> occurred relatively seldom.

I would really like to see an example of input and output files to try and
understand what happens there. The poblem may be related to PBCs and
coordinate wrapping, but cannot be certain without looking at it more

Best regards,

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