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

Berk Hess gmx3 at hotmail.com
Fri Jun 6 09:45:13 CEST 2008

From: gmx3 at hotmail.com
To: bjorn.sathre at student.uib.no
Subject: RE: [gmx-users] Possible issues with CVS pull code 200800508
Date: Fri, 6 Jun 2008 09:41:36 +0200


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
> 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:
> pullforces.xvg
> 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  
> stability?
> Determinig the COM forces along z with g_traj I get the output of:
> forces.xvg
> 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
> appreciably?
> Regards
> -- 
> Bjørn Steen Sæthre
> PhD-student
> Insitute of Physics & Tech.- University of Bergen
> Allegt. 55,
> 5007 Bergen
> Norway
> Tel(office): +47 55582869
> Cell:        +47 99253386
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