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

Mark Abraham mark.j.abraham at gmail.com
Sat Sep 21 14:12:17 CEST 2013

You can try a run in implicit solvent to get a feel for the maximum
diameter of the protein while unfolding. You will not have any
certainty unless you can afford a box whose diameter is that of the
straight-line peptide...


On Sat, Sep 21, 2013 at 1:03 PM, aksharma <arunsharma_cnu at yahoo.com> wrote:
> 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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