[gmx-users] Re: Adsorption layer of water molecules

Justin Lemkul jalemkul at vt.edu
Fri Feb 8 17:28:05 CET 2013

On 2/8/13 11:25 AM, ypca wrote:
> The increase of the box volume occur in the beginning of the npt
> equilibration. The analysis of pressure was like that:
> Pressure nvt = fluctuates between 500 bar
> Pressure npt = fluctuates 1 bar
> Pressure in production stage = fluctuates 1 bar
> Actually, the problem is that water molecules go very far away from the
> protein.
> These are links to the images of the protein in water, one view close and
> another with a smaller zoom. It's like the box has exploded and water has
> became free, like no interactions occur between the protein and water.
> http://www.dta.ufv.br/arquivos/proteinaway.png
> http://www.dta.ufv.br/arquivos/proteinclose.png

Please post a complete .mdp file and the box vectors of your starting and ending 
configurations.  In reality, the system probably should have exploded and failed 
to run.  You did not do any post-processing with trjconv, correct?  The output 
you have shown is the actual mdrun output, yes?



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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