[gmx-users] all atom force field
sunnytov at hotmail.com
Tue Jun 21 17:25:15 CEST 2005
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
Here is my question. Is it a good or ever plausible idea to introduce new
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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