[gmx-users] ffgmx for lipids

[strony_w_w_w at op.pl]

An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20050104/e86bfe5c/attachment.html>
-------------- next part --------------
1. 

 

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

http://moose.bio.ucalgary.ca/Downloads/

 

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? 

 

2. 

 

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.