[gmx-users] bilayer leaflets separating

[Xavier Periole]

David van der Spoel wrote:

>On Fri, 2004-11-12 at 07:21 -0500, Amadeu wrote:
>  
>
>>Tsjerk and Florian,
>>
>>Thank you for your comments. When I do apply the "-pbc nojump" option,
>>I do get the bilayer to  visually look correct, but what concerns me
>>is that the Z-dimension (normal to the bilayer interface) is very
>>large and does not seem to stabilize. The bilayer and water are only
>>about 10 nm, but box size is about 20 nm and its continues to increase
>>as through the simulation. Is this what you have observed too? Any
>>idea why the box size in the z-dimension expands like that?
>>    
>>
>Maybe you could try running the CVS code, there was recently something
>related to PME that is magically fixed in the CVS code. You could also
>try to run with cut-offs for a while for testing.
>
The problem is likely to be in the definition of the pressure coupling 
you use !!!
NPT is ok but isotropic, semiisotropic, anisotropic ?? You have to 
include different
number of values depending on the ???tropic you chose.
XAvier

>  
>
>>Thanks,
>>
>>                     Amadeu
>>
>>
>>On Fri, 12 Nov 2004 10:34:39 +0100, Tsjerk Wassenaar
>><t.a.wassenaar at chem.rug.nl> wrote:
>>    
>>
>>>Hi Amadeu,
>>>
>>>Are you by chance observing the jumping across the periodic boundary?
>>>That's only a virtual thing.
>>>Try running the trajectory through trjconv with the '-pbc nojump' option.
>>>
>>>Tsjerk
>>>
>>>
>>>
>>>Amadeu wrote:
>>>
>>>      
>>>
>>>>I am experiencing something very strange: the leaflets of my bilayer
>>>>are continuosly separating, thus creating a large gap in the middle of
>>>>the bilayer. I ran the simulation for 100 ps and the gap was about 10
>>>>nm. I tried this same simulation many times, in several machines, and
>>>>I cannot get it to be stable. Would anyone have any idea what may be
>>>>the problem? This is a simulation for a small bilayer with 64 and 3846
>>>>water molecules (from Tieleman's webiste). The simulation are in the
>>>>NPT ensemble (1 bar and 323 K), with 1.0 nm and 1.8 nm cut-off for the
>>>>LJ and eletrostatic interactions, respectively. Periodic conditions in
>>>>all directions. The initial velocity were generated at the start of
>>>>the simulation. I am using the GROMOS forcefile for the lipid and SPC
>>>>water. The strangest thing is that I can use this same forcefield and
>>>>conditions for the simulation of a large bilayer (128) and I do not
>>>>encounter this problem. I would greatly appreciate input/comments.
>>>>
>>>>Thanks,
>>>>
>>>>               --Amadeu
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>>>>
>>>>        
>>>>
>>>--
>>>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>>-- :)
>>>-- :)   Tsjerk A. Wassenaar, M.Sc.
>>>-- :)   Molecular Dynamics Group
>>>-- :)   Dept. of Biophysical Chemistry
>>>-- :)   University of Groningen
>>>-- :)   Nijenborgh 4
>>>-- :)   9747 AG Groningen
>>>-- :)   The Netherlands
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>>>      
>>>
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-- 
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   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole
   
----------------------------------------------