On 2014-05-09 13:47, Piggot T. wrote:
Hi David,
Firstly I would say, is there any reason why you need to use the
Berger/Höltje/GROMOS force field combination? There are several other options
available that I can think of which may be easier/better for you. You could use
the Slipids (with an AMBER force field for the protein), CHARMM36 for all of
the components of your system, or if you do want to stick with a united-atom
force field, you could still use one of the GROMOS force fields ((e.g. 54A7)
with the GROMOS-CKP lipids and the consistent cholesterol parameters that you
can download from the manual entry of the automated topology builder. I haven't
ever simulated cholesterol so I cannot really recommend which may be better
than others for this molecule, but there will be plenty of literature out there
to look at regarding this.
Secondly, if you do want to stay with the Berger/Höltje/GROMOS combination, you
could probably add the missing atomtypes to the GROMOS force field you wish to
use. I would strongly advise against using the old 'ffgmx' force field, this
has been shown to behave pretty poorly for proteins. Do be careful in doing
this addition of atomtypes, as the GROMOS force fields are different from the
all-atom force fields in as much as the atomtypes have multiple van der Waals
interaction parameters used for interactions with different atomtypes. Some of
the GROMOS papers describe this in far more detail.
Just some of my thoughts, hopefully of some use!
You could also look here:
http://cmb.bio.uni-goettingen.de/downloads.html
Cheers
Tom
--
Dr Thomas Piggot
University of Southampton, UK.
________________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Ollila Samuli
[samuli.oll...@aalto.fi]
Sent: 09 May 2014 11:42
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Force Field for Bilayer Simulations with Cholesterol
and Proteins
Hi,
I used ffgmx.itp. It contains CB.
BR,
Samuli Ollila
________________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of David Ackerman
[da...@cornell.edu]
Sent: Wednesday, May 07, 2014 10:30 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Force Field for Bilayer Simulations with Cholesterol
and Proteins
Thank you for your advice.
Which force field was used? I have downloaded the cholesterol parameters
from Höltje et al, but atomtypes like CB do not exist in the force field I
am using (53a6). Did you change these to other atomtypes as well, or were
you using a force field that included them?
-David
On Wed, May 7, 2014 at 8:59 AM, Ollila Samuli <samuli.oll...@aalto.fi>wrote:
Hi,
In my understanding the CH2-LP2 attraction is stronger than LP2-LP2
attraction in the Berger/Höltje combination you described. If you then have
CH2 groups in cholesterol and LP2 groups in lipids, it might lead to too
condensed bilayer. I think that the related issue is discussed here:
http://dx.doi.org/10.1088/0953-8984/18/28/S07
and here:
http://dx.doi.org/10.1039/C2CP42738A
we have changed the CH2 groups in cholesterol to LP2 groups and compared
the results quite extensively to the NMR measurements.
BR,
Samuli Ollila
________________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of David
Ackerman [da...@cornell.edu]
Sent: Monday, May 05, 2014 7:39 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Force Field for Bilayer Simulations with Cholesterol
and Proteins
Hello,
I have been performing simulations of multi-component bilayers using
parameters described in the following paper:
http://www.ncbi.nlm.nih.gov/pubmed/23470157. They use the ffgmx forcefield
with Berger lipid parameters included. They also use cholesterol from
Holtje et. al (
http://www.sciencedirect.com/science/article/pii/S000527360100270X), which
was parameterized for the ffgmx force field.
I noticed that unlike the KALP-15 GROMACS tutorial which suggests deleting
the default lipid-gromos Berger interactions, the authors kept those
interactions in the force field. In light of newer force fields, are these
older force fields wither Berger parameters still acceptable? The
cholesterol model seems commonly used, so I am unsure how to use
cholesterol with a newer force field.
Furthermore, if I were to include proteins in the simulation, would I still
be able to use the same ffgmx force field with Berger parameters (including
lipid-gromos interactions)?
Thank you,
David
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
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