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,
Regards,
Alok.
----- Original Message -----
From: "Mark Abraham" <[EMAIL PROTECTED]>
To: "Discussion list for GROMACS users" <gmx-users@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
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.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
