[gmx-users] OPLS + ffgmx

Mark Abraham mark.abraham at anu.edu.au
Wed Sep 6 04:17:51 CEST 2006

> Hi all,
> I am trying to do a membrane protein simulation. I want to use OPLS - AA
> force field for protein and ffgmx (modified ffgmx force filed with lipid
> parameters from user contribution section ) force field for POPE lipids.
> Is it is possible and advisable to use two different force fields for
> protein and lipids?

In general, this way madness lies. Force fields are mathematical
constructs that are optimized to approximately reproduce some experimental
properties *in cooperation with itself*. There is no reason to expect that
force field parameters for "bond strength" have any great correlation with
an experimentally determined bond strength, and thus to have no
correlation with a "bond strength" from another force field. Accordingly
there's no reason to expect that a mixture of parts of different force
fields will work well together. It's somewhat like taking half of a soccer
team and half of a gridiron team and expecting them to be able to play
rugby together.

> Or else, Is there any all atom force field availble for lipid molecules
> which I can use?

CHARMM parameter sets optimized for combined protein & lipid calculations
exist. Simplest would then be to use CHARMM or NAMD. If you want to use
GROMACS, you can get such a force field, use my scripts available here
http://www.gromacs.org/contributed_by_users/task,doc_details/gid,59/ to
convert them to gromacs format, obtain some .rtp files elsewhere, test
carefully, and simulate to your heart's content.


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