[gmx-users] OPLS + ffgmx
alokjain at iitk.ac.in
Wed Sep 6 21:48:47 CEST 2006
Hi Mark and Chris,
Thanks a lot to both of you for going through my query, for suggesting the
positive and negative points of this procedure.
I will think and then decide how to go about it.
I am really thankful to Chris for the detailed suggestion regarding the
procedure. I will come back to you later as I go about it.
Thanking you all again,
----- Original Message -----
From: "Mark Abraham" <mark.abraham at anu.edu.au>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Wednesday, September 06, 2006 7:47 AM
Subject: Re: [gmx-users] OPLS + ffgmx
> 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
> 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
convert them to gromacs format, obtain some .rtp files elsewhere, test
carefully, and simulate to your heart's content.
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