[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.
Thanks,
Pramod
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