[gmx-users] Compressing bundles of fibers into a surface
pbuscemi at q.com
Fri Jul 20 01:09:05 CEST 2018
Dear gmx users
I’m in the process of creating a PE polymer surface.
pdb and itp files were obtained from ATB and were used to produce a (xyz) 142 x 6 x 60 A box ( starting size ) with 300 150 A long molecules.
They were neatly aligned to start and - using pcoupletype = surface-tension and a restraint on the x direction ( fc=10) they stay aligned through md but are now in bundles - which is what they should do
But now I want to compress ( move them in the y direction ) the bundles into a 142 x 6 x say 20 A box. i.e. a more or less complete surface
I’ve tried re-running npt on the first md result, with no change. (10 ns md) Making a smaller box ( smaller y) with confedit and running npt or md leads to very High PE.
Other than waiting for the cows to come home using md,, could a suggestion be made to coerce the bundles to come together ?
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