[gmx-users] ffgmx for lipids

strony_w_w_w at op.pl strony_w_w_w at op.pl
Tue Jan 4 17:04:32 CET 2005

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I&#8217;m simulating some different types of membranes using ffgmx for

lipids from gromacs site.


  I plan to use some of the  lipid structure and topology files from



When I was doing EM and MD of membrane made of POPE lipids I noticed

something strange: distance between atoms H1 and O7 was about 1.3 A for

every lipid.


  I&#8217;m not sure if this is correct.  Did someone use this pope.pdb and

pope.itp file? 




I don&#8217;t understand why are the parameters for L-J interactions of atom   

types LOS - LNL (in Ffgmx_lipids) different from parameters for OS - NL 

interactions (in ffgmx).  (the same is in case LOM-LOM and OM &#8211; OM)  Should I use parameters from ffgmx for the atoms building head of the lipid in order to keep the right geometry.   


 Please give me some comment. 

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