Joshua Ballanco wrote:
Hello all,
Apologies if this is obvious, but I've been reading through the manual
and various Google searches and come up empty-handed. My question is if
it is possible to construct an infinite polymer chain in Gromacs? That
is, I'd like to setup a cell with PBC, but have one end of my molecule
bound to its replica across the boundary. As far as I can tell, adding
extra bond records to the topology always turns my polymer into a loop
in one cell.
Depending on your Gromacs version, the approach will be different. Under 3.3.x
you can use "pbc = full," and provided that your topology is correct, you will
get an infinite molecule. Under 4.x (if I understand the changes correctly),
you should be able to set "periodic_molecule = yes" in conjunction with "pbc = xyz."
-Justin
Thank you for any advice.
Sincerely,
Joshua Ballanco
Graduate Student
Department of Chemistry and Chemical Biology
Stevens Institute of Technology
Hoboken, NJ 07030
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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