[gmx-users] all atom force field

이 선주 sunnytov at hotmail.com
Tue Jun 21 17:25:15 CEST 2005

Hello All!

I am trying to parameterize a small molecule so that I can do the md 
simulation it with lipid bilayer.
The problem I have is that I have to use the gromax united force field for 
the lipid bilayer part but I need 
all atom force field for the small molecule. Especially my small molecule 
has a short alkane chain of 
three carbon atoms. So now I had to introduce new atom types for alkane 
carbon and hydrogen atoms 
to the gromax force field. I adopted parameters from oplass force field and 
ffgmx2 force field and modified ffgmx.atp, ffgmxnb.itp and ffgmxbon.itp 
files and finally could minimize the molecule 
and start md simulation, but after several ps the molecule blew up. 
I started the md simulation from a single minized structure at very low 
temperature and in vacuo.
I think the parameters were not accordant with the parameter sets in ffgmx 
force field. 

Here is my question. Is it a good or ever plausible idea to introduce new 
atom types 
into the gromax force field and to simulate alkane hydrogen explicitly?
If yes, can you suggest me ways to get the right parameters for new atoms 
If not, do I have to generate rtp file for my small molecule and use dummy 
atoms for hydrogen atoms? In this case, should I use ffgmx2 force field or 
still can I use ffgmx force field?

I am looking forward helps.

Thanks in advance

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