How to prevent cg water entering a membrane

From: Francesco Pietra (
Date: Fri Dec 18 2009 - 16:49:55 CST

I succeeded in minimizing (thus const volume) a coarse grained
protein+bilayer in a cg water box, finishing with a short MD,
hopefully to bring the system to 300K. For equilibration (thus const
pressure and 310K) are

margin 3 (allow large volume fluctuations)


tclForcesScript keep_water_out.tcl (prevent water entering the bilayer)

needed like in a all-atoms equilibration? If so, does the script
"keep_water_out.tcl" understand the job with cg systems?

constraints on
consexp 2
consref kcsa_popcwi.pdb
conskfile kcsa_popcwin.cnst
conskcol B
margin 3
tclforces on
set waterCheckFreq 100
set lipidCheckFreq 100
set allatompdb ../02-MEMBRANE/kcsa_popcwi.pdb
tclForcesScript keep_water_out.tcl

francesco pietra

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