[gmx-users] question about all atoms lipid molecule

Pär Bjelkmar bjelkmar at cbr.su.se
Fri Oct 16 13:22:53 CEST 2009


> I need to do an all atom simulation for dppc bilayer . You are right  
> the
> dppc molecule file that i have has PALM and PCGL residues.
Well, I don't know where you got the dppc molecule from, I thought you  
said you didn't have any DPPC structure with hydrogens? Anyway, I'll  
send you the current version of the charmm force field for GROMACS (in  
a separate e-mail) but I'm afraid I cannot help you in building the  
residue. I think it might be quite a lot of work if you don't know how  
CHARMM is doing it. My suggestion is that you search/ask the CHARMM  
mailing list for how DPPC is constructed.

> I will like to try to set up the charmm FF for gromacs. But I dont  
> have the
> FF files with me, neither do i have the programs. Could you send me a
> tutorial or some reference link too ( if you know of any).
What you need for running CHARMM ff in GROMACS are the files I'll send  
you and the latest version of the source code (i.e. do a git pull and  


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