[gmx-users] Possible issues with CVS pull code 200800508
Bjørn Steen Sæthre
st01397 at student.uib.no
Thu Jun 19 13:49:25 CEST 2008
Dear Berk (and whoever else might provide assistance)
I have included also my topology file topol.tpr at
From this you can clearly see that there is no pressure coupling in my
I still have not resolved the issue of the fluctuation artefacts.
Berk, you state that the position should not fluctuate. To that I can
add that the relative position between the pull group and the
reference stays very nearly constant. However, the absolute movement
along the z-coordinate of the entire system in the box becomes all too
large, but not large enough to impinge upon the walls during
simulation. This large absolute movement of the pull group can be
clearly seen in the file
However, this output is also slightly misleading in that the
fluctuations as found in the trajectory are not nearly as large as
those found in the above file. I seriously doubt if this discrepancy
is solely due to aliasing by differing sampling frequencies in the
trajectory frame output vs the pull-code output.
You stated that neither altering time-step or the constraint-strength
would change the situation. Then I guess the only thing remaining
would be the geometry of the system.
I wish to maintain roughly the same number of atoms.
Do you think it might be an idea to adopt a thinner slab-geometry.
That is increase the area of contact between the slabs, while reducing
the slab thickness in the direction of pull? What effects do you
expect from this alteration?
I appreciate clarification from anyone competent in these matter.
Quoting Bjørn Steen Sæthre <st01397 at student.uib.no>:
> Dear Berk,
> Yes, I use the walls only to allow efficient neighboursearch and to be
> able to utilize PME.
> You state that I pressure-couple in z, although I have put pcoupl=no
> and commented out the rest of the p-coupling parameters by initial
> semicolons in these lines.
> Have you changed the commenting style of the mdp-files recently? Or did
> you just miss this detail in my mdp-file? (You are correct that I have
> not put the compressibilities to 0, but I have commented out the line!
> Haven't I?)
> Do you need additional files to diagnose the problem?
> Quoting Berk Hess <gmx3 at hotmail.com>:
>> Larger time step or higher constraint will not help.
>> I assume you do not need the walls for interactions,
>> you only use them for efficient neighbor search, right?
>> The distance should not fluctuate at all, so there is something very wrong.
>> One problem is that you pressure couple in z.
>> This might be the cause of all your problems.
>> Try setting the compressibility in z to zero.
>>> Date: Thu, 5 Jun 2008 13:42:39 +0200
>>> From: st01397 at student.uib.no
>>> To: gmx-users at gromacs.org
>>> Subject: [gmx-users] Possible issues with CVS pull code 200800508
> Bjørn Steen Sæthre
> Insitute of Physics & Tech.- University of Bergen
> Allegt. 55,
> 5007 Bergen
> Tel(office): +47 55582869
> Cell: +47 99253386
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Bjørn Steen Sæthre
Insitute of Physics & Tech.- University of Bergen
Tel(office): +47 55582869
Cell: +47 99253386
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