[gmx-users] Membrane issues
haerterich at apollo1.pharmazie.uni-erlangen.de
Wed Jul 14 15:45:31 CEST 2004
after browsing around the manual and mailing list archive I am rather
confused about which forcefield to use for a protein/water/bilayer
The standard GROMACS or the ffgmx43a2x?
Another problem: The lipid.itp from Tieleman is said to be included
within the GROMACS-Forcefield. There also exists a building block for
DPPC. However there are no bonds specified within the ffgmx.itp for
CH3-NL as should be (these are used in the DPPC building block).
The same is true for some angles.
On the other hand the dppc.itp file alone does not work as #include
within the topology-file for some atom types are not defined. So there
are some atomtypes being defined twice with the lipid.itp included
and others missing without the lipid.itp.
Is this true or did I just stupidly oversee some major detail?
Is there some "ready to use" and easy way to build a nice little bilayer?
Thanks a lot for your answers.
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