[gmx-users] Re: Minimum distance periodic images, protein simulation

aksharma arunsharma_cnu at yahoo.com
Sat Sep 21 13:03:46 CEST 2013

Hi Justin,
Thanks for your reply. I have some follow-up questions. Since the simulation
is high temperature (450 K) there is slight unfolding of the protein. 

The box was set up as rhombic dodecahedron with 1.2 nm as the distance
between solute and edge of box. 

pdb2gmx -f 1L2Y.pdb -o 1L2Y-processed.gro -ignh -water spce

The cutoffs are 0.9 nm for VDW and electrostatics. 

Do you suggest using an even bigger box for studying unfolding? Or is there
something else that could be going on? Do you have any ball park suggestions
for a good size of the box or is this something that I would have to
experiment with different sizes until I land a suitable box.

Thanks a lot,

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