[gmx-users] POPC bilayer with Charmmff

ram bio rmbio861 at gmail.com
Sat Oct 22 00:10:36 CEST 2011

Dear Gromacs users,

I have downloaded the POPC bilayer molecular coordinates with charmmff
equilibrated from Dr. Klauda's website. In this site it is mentioned

Note: If you run these simulations in NAMD you MUST use NAMD 2.7b3
with vdw ForceSwitching turned on;

what does vdw ForceSwitching turned on mean, is it related to adding
few more parameters to mdp files? like

rlist           = 1.2
rlistlong       = 1.4
rcoulomb        = 1.2
rvdw            = 1.0
vdwtype         = switch
rvdw_switch     = 0.8
coulombtype     = PME
pme_order       = 4
fourierspacing  = 0.16

and , does this apply to gromacs also, if i use these lipid bilayers
to run simulations in gromacs.

I have one more question, i want to increase this bilayer containing
72 lipids to 250 lipids, so how can i do this or can i get it
downloaded from any website like Dr.Klauda website

Please let me know your suggestions.



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