[gmx-users] problem with undistribution of water

Mark Abraham Mark.Abraham at anu.edu.au
Fri Mar 7 06:31:45 CET 2008

sudheer babu wrote:
> Thanks Mr .Justin for your response,
> I am describing answers for  your questions,
> 1.My box size is 6.0nm in xyz dimensions.
> 2.The forcefield  I am using "ffgmx.itp" for membrane which I downloaded 
> from Pieter Tieleman webiste and deprecated FF for protein.
> 3 .I inserted protein into membrane by using genbox command.
> 4. I used force constant 10000 on protein.
>   There is no leaking of membrane, the stucture is fine till EM, but in 
> PR the water molecules are moving from one side of the bilyaer to the 
> other side. No water mol between lipid bilyer hydrophobic region. Ok I 
> tell you in clear way, Assume on membrane  each side 200 water molecules 
> are there but after equilabration 30 to 50 water molecules are reaching 
> other side , so one side its appearing  more  rather than other side.  
> But it looks in cubic form how appears in EM but only increasing water 
> molecules on other side. Popc and protein are fine. Will it cause any 
> problem later when I run further simulation by taking this output file.I 
> hope you got my problem.

There's no rule that says the simulation should preserve equal numbers 
of waters on each side of the membrane. Because the system is periodic, 
there's only one chunk of water, and one chunk of membrane. Any 
translated representation of this system is as good as any other for 
numerical purposes. If you care how your output looks, this is what the 
options to trjconv are for. I'm sure I've answered this question once a 
month for the last year or so :-)


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