[gmx-users] Compressing bundles of fibers into a surface

paul buscemi 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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