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

Bjørn Steen Sæthre st01397 at student.uib.no
Tue Jun 10 11:11:28 CEST 2008

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>:

> Hi,
> 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.
> Berk.
>> 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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