[gmx-users] Reliability about Lipid Order Parameters in GROMACS
T.Piggot at soton.ac.uk
Mon Sep 7 18:38:52 CEST 2015
I would have thought you might be better, for an all-atom lipid force field, in modifying the CHARMM force field based VMD tcl script. I believe g_order is intended for united-atom lipids and so predicts the positions of the hydrogen atoms based upon an idealised geometry. This isn't ideal for an all-atom force field as you will miss things like any potential splitting of the order parameters for the hydrogens on carbon 2 in the sn-2 chain.
Give my best to Angel.
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Rebeca García Fandiño [regafan at hotmail.com]
Sent: 07 September 2015 11:06
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Reliability about Lipid Order Parameters in GROMACS
Thank you very much
for your suggestions, Tom.
In fact, Ángel and me
are collaborating in this work :)
We are using AMBER,
not CHARMM, this is why we wanted to know if the error about order
parameters had been corrected in the new versions of GROMACS.
I will try the patch
Justin suggested before modifying the scripts for AMBER.
> Date: Fri, 4 Sep 2015 01:05:47 +0100
> From: t.piggot at soton.ac.uk
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Reliability about Lipid Order Parameters in GROMACS
> Hi Rebeca,
> The patch linked to by Justin (provided by Chris Neale) does work fine
> in my hands (well I tested it for the unsaturated double bond in POPC at
> least). If you are using the CHARMM36 force field, there is a VMD tcl
> script out there that can be used. As for the script that was made for
> the work you linked to, Angel Pineiro (who is also at USC) made this
> (although if I remember correctly it was pretty slow in calculating the
> order parameters). I'm sure he'd be happy to share, if you so wished.
> On 03/09/15 21:37, Justin Lemkul wrote:
> > On 9/3/15 3:40 PM, Rebeca García Fandiño wrote:
> >> Dear GROMACS users
> >> I have a general doubt
> >> about the reliability of calculating order parameters for lipids
> >> containing saturated and
> >> unsaturated chains. For example, DOPC (attached). The order parameters
> >> for the two chains are too similar and however one of them is
> >> saturated and the other one unsaturated.
> >> If you notice the
> >> paper J. Chem. Theory Comput., 2012, 8 (11), pp
> >> 4593–4609 (http://pubs.acs.org/doi/full/10.1021/ct3003157),
> >> the authors determined deuterium order parameters using locally
> >> written code because
> >> the GROMACS program g_order did not provide the correct order
> >> parameters for
> >> carbons in the unsaturated double bond of the POPC oleoyl tail
> >> (versions 4.0.7
> >> and 4.5.1 of g_order were tested). I have tried version GROMACS
> >> 4.6.2 and
> >> GROMACS 5.0 for my DOPC system and the
> >> results are very similar between both versions, so I think this supposed
> >> error has not been corrected in the new versions of GROMACS.
> >> Could anyone clarify
> >> if Deuterium Order parameters are well calculated for the unsaturated
> >> double
> >> bond of lipids in GROMACS?
> > Try the patch here:
> > http://redmine.gromacs.org/issues/1166
> > But no, there has been no action on this issue in many years.
> > -Justin
> Dr Thomas Piggot
> University of Southampton, UK.
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