Hello,
I am developing a oil model compose by hydrocarbons molecules (low
weight), but I have some problems when I simulate to reproduce the
experimental density. I am using the last version of CGenff
parameters.
I do not know if I am using wrong parameters or my topology file are
not correct described.
For bonds/angles/dihedrals description I am using a molecule in mol2
format file, then I convert to MDynamix mmol file and finally write in
a LAMMPS topology file.
I would like to ask if I can use a better methodology do describe the
molecules or if cgenff can reach the experimental density for
hydrocarbons.
Thanks in advance!
Hello,
I am developing a oil model compose by hydrocarbons molecules (low
weight), but I have some problems when I simulate to reproduce the
experimental density. I am using the last version of CGenff
parameters.
I do not know if I am using wrong parameters or my topology file are
not correct described.
For bonds/angles/dihedrals description I am using a molecule in mol2
format file, then I convert to MDynamix mmol file and finally write in
a LAMMPS topology file.
I would like to ask if I can use a better methodology do describe the
molecules or if cgenff can reach the experimental density for
hydrocarbons.
the latter part of your question is particularly something that you have
to query the published literature for. since cgenff is a rather generic
parameterization strategy, you will have to expect limited accuracy and
transferability.
if you want a better correspondence to experiments, you may need to look
for more specific parameterizations. again, that is something to search for
in the literature. that is why people write those papers (to advertise they
findings and provide discussions or accuracy and applicability or models).
axel.