[gmx-users] Possible issues with CVS pull code 200800508

Bjørn Steen Sæthre st01397 at student.uib.no
Thu Jun 5 13:42:39 CEST 2008

I am doing Constraint force pulling to measure the cohesive force
between two rectangular slabs of a certain material. The slabs are
made effectively infinite in the directions normal to z, using pbc=3Dxy,
I have to use walls to be able to exploit PME eletrostatics. To
accomplish this I have to use walls in the z-direction
My box size is 3.4x3.4x15 nm, the two slabs are each slightly
elongated rectangular "prisms" 3.4x3.4x5.1 nm, comprising about 7500 =20
atoms each separated by say, 1 nm  initially. Thus about 1/3 of the =20
box was vacuum outside the "external" faces of the slabs.

My auxiliary files are stored at http:/drop.io/gmxpull

My paramater-file is eq_pull.mdp

During the course of the simulation, the slabs stay separated at all
times, but show appreciable oscillation in distance the constraint
forces between the COM's of the two slabs show the peculiar behaviour
shown in the file:


It seems as if the constraint forces simply becomes to great,  
especially at short separations, and
makes the system unstable. Should I increase or decrease the pull_constr_tol
to improve the stability of force readouts in my large system? I would  
presume increasing the tolerance would promote less fluctuations in  
forces, and larger distance fluctuations?
I know that the constraint Force is calculated as F = M (dr)/(dt)^2,  
where dr is the adjustment made by the constraint algorithm(SHAKE) and  
dt is the time-step during which the constraining takes place. This  
leads me to anticipate that maybe a larger time-step would promote  

Determinig the COM forces along z with g_traj I get the output of:


Why the strange behaviour of the constraint forces?
Why the extreme peaks in forces? Why does the constraint force output
and the output of force z-coordinate in "g_traj -com -nox -noy", differ so


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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