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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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