[gmx-users] Re: Constraints not working in pull code (sometimes, sometimes not)

Krapnik krapnik at gmail.com
Thu Aug 11 09:53:24 CEST 2011

Dear Justin
Thank you for your responses, but it still is not clear to me why is that

> I don't see any real problem here.  The DOPC membrane probably holds its
> better than the octanol slab and thus the reference position (which
> the constraint) is less mobile.

That is certain. When we were running free simulation, the box started to
narrow. Therefore we have frozen the box in xy plane.

> As such, the constraint is more stable in DOPC
> than in octanol.  The slight bump in the octanol system amounts to a
change of
> 0.16%, which I'd say is quite small.

The trouble is, that during next 10 ns the distance was between 2.0 - 4.0
and molecule moved outside of the ocatnol slab and inside, which is then
useless for calculation of PMF.

> You're also looking at the first few
>frames of the simulation, which may amount to equilibration, but you
> mentioned if you've done anything prior to this run.

Previously, a free simulation with molecule on slab was run for 20 ns, from
which frame with small molecule at specidied depth was taken, so I suppose,
that the start is equilibrated.

> As long as there is no systematic change in position, I'd say there's no

Unfortunately, there is as I have said before.


Dear Chris,
thank you for responses as well.

> I agree that Justin is probably correct, although constraints should
> technically work just fine with a highly dynamic reference group. Any
> problems should show up as the system blowing up, but not in correctly
> setting the position.

I hope, that the position is set up ok, as it stays steady in DOPC.

> I think that the problems can arise, however,
> when you have multiple competing constraints. You might, for example,
> try without constraining the octane bonds -- I think that you should
> get perfect match in that case.

I will try.
The erroneous movement of molecule seems to be enhanced within XY-plane
The curious thing is however, that when I did not constrain size of
xy-plane, then the distance to the COM of slab is not changing much (only
last digit changes), which in comparison to frozen XY-plane, where there is
huge movement above the slab and within is rather ok to me. Unfortunately, I
have the issue with narrowing of the box in the unconstrained XYplane
simulation, which also destroys any attempts for PMF as I have mentioned

> Also, it is worth comparing in single
> and double precision.

I will try this either.

> Still, I am not sure that you actually did a proper comparison for the
> following 2 reasons:
>1. you have apparently different masses for the pulled group:
> Pull group 1:    15 atoms, mass   194.194
> Pull group 1:    15 atoms, mass   146.146

The difference is not much in my opinion, while molecules tested are similar
in size and are run in DOPC ok both of them.

> 2. you used very different starting depth offsets: -2.81855 is not
> very close to -1.60929

The difference is in the size of OCT slab (thick) and DOPC (narrow) and the
trouble is in the vicinity of the water phase, so the distances are (and
should be) different.

> PS: I would personally prefer if you avoided jumping directly to a bug report
unless you are sure of it. There is always at least the
> possibility that you are not using the code correctly.

Certainly and I appreciate two directions you gave me to try - at least I
will look inside octanol topology since I did not used octanol before our
tries of logP. However, I did not say anything about bug (I even searched
for term in my mail and I did not find it)

But how to set the box properly then?

> Chris.

Thank you both

Zdraví skoro zdravý
Karel "Krápník" Berka

RNDr. Karel Berka, Ph.D.
Palacký University in Olomouc
Faculty of Science
Department of Physical Chemistry
tř. 17. listopadu 1192/12
771 46 Olomouc
tel: +420-585634769
fax: +420-585634769
e-mail: karel.berka at upol.cz

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