[gmx-users] Protein going out of the box

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Jul 15 12:24:35 CEST 2009

Think outside of the box when using Periodic Boundary Conditions. :p


On Wed, Jul 15, 2009 at 9:14 AM, Mark Abraham<Mark.Abraham at anu.edu.au> wrote:
> nikhil damle wrote:
>> Hello,
>> When I am running energy minimisation of protein-peptide complex,
>> minimised structure shows a space for the protein in water box; but peptide
>> remains inside the box while protein is seen outside.
>> Same occurs when I keep pbc = xyz and/or nstcomm = 1
>> in ..top file, I am including individual posre.itp files (posre_A.itp and
>> posre_B.itp) separately.
>> How should I fix this problem ?
> See this page, in particular the bottom.
> http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions
> Mark
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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