[gmx-users] Lipid Bilayer questions
Ramachandra Rao Gullapalli
rrg142 at psu.edu
Tue Mar 1 16:33:42 CET 2005
I am still getting my feet wet with MD simulations.I had a few questions
1) Which is the best force field to use for a DMPC bilayer?
2) If i used the DMPC.itp from Dr Tieleman s site, where do i need to save it in
order for the pdb2gmx,edit conf etc to work....that is, do i need to save it in
the "top" folder or do i need to place it in the specific forcefield file for
it to work?
3) How do i create a DMPC.top file and DMPC.gro file? (I mean are there any
DMPC.pdb files out there?)
4) I tried using pdb2gmx on Dr Tieleman s DPPC64.pdb,and ended up getting 26
(A-Z) posre.itp files and DPPC_A.itp -DPPC_Z.itp(ANother 26).Is it necessary to
create all these files seperately? BUt since there are 64 lipids, what about
the other lipids? Is it necessary to create posre files for every individual
5) Are there any good resources out there which describe how to setup a bilayer
simulation,Since i am working this out all on my own, i dont have anyone to
discuss this with.
Id appreciate any answers and thank you all for your time.
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