[gmx-users] membrane model

Piggot T. T.Piggot at soton.ac.uk
Mon Jun 22 12:19:50 CEST 2015


If you check out the second paper I linked to before ( the shameless plug to my own work!), this should give you a good idea. That said, this work is a from a few years ago now so there are some other parameters that are also now available (google should find them for you).

Cheers

Tom

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of anu chandra [anu80125 at gmail.com]
Sent: 22 June 2015 11:10
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] membrane model

Thanks to all for the useful replies. BTW, which force field will be good
option for simulating united-atom (acyl chain) POPC membranes?

Many thanks
Anu

On Fri, Jun 19, 2015 at 5:15 PM, Thomas Piggot <t.piggot at soton.ac.uk> wrote:

> Good to see the membrane structures have been changed/fixed. I think it
> was December 2010 when I last downloaded the POPC one!
>
> I did port over the lipid parameters for C27-UA a good while ago but
> haven't got around to the C36-UA parameters yet.
>
>
> On 19/06/15 16:55, Justin Lemkul wrote:
>
>>
>>
>> On 6/19/15 11:38 AM, Thomas Piggot wrote:
>>
>>> Well, the CHARMM ff is not entirely all-atom:
>>>
>>> http://pubs.acs.org/doi/abs/10.1021/jp410344g
>>>
>>>
>> True, people have developed UA force fields from CHARMM's all-atom
>> models.  My comment was largely motivated by the fact that the official
>> CHARMM36 port for GROMACS is based entirely on all-atom models.  If one
>> wants to use CHARMM36-UA in GROMACS, the force field parameters will have
>> to be ported over.
>>
>>  As for downloading the structure, I would be slightly careful with the
>>> link that
>>> Justin provided for POPC as (well, based upon the last time I used it
>>> anyway)
>>> there were a different number of lipids in each leaflet of the membrane
>>> (65/63).
>>>
>>
>> That doesn't appear to be the case with either of the POPC membranes
>> currently available for download.  64 in each, at least according to gmx
>> select :)
>>
>> -Justin
>>
>>  Plus, you should also be aware that the topology on this site is not
>>> quite the
>>> same as that described by Berger et al. If you are interested, see this
>>> shameless plug to my own work for more details about this:
>>>
>>> http://pubs.acs.org/doi/abs/10.1021/ct3003157
>>>
>>> We had intended to make all our structures, etc. from this work
>>> available online
>>> but never quite got around to it. If you need a particular structure,
>>> send me an
>>> off list email and I can try and help.
>>>
>>> Finally, as for using the CHARMM-GUI, Justin is correct that it won't
>>> provide
>>> you a united-atom membrane straight out of the box. However, a simple
>>> script can
>>> be used to strip out the hydrogens and rename the atoms, should you
>>> really wish
>>> to use it to build your membrane system (I have done this before for
>>> converting
>>> DPPC/POPC membranes to a range of different united-atom force fields).
>>>
>>> Cheers
>>>
>>> Tom
>>>
>>> On 19/06/15 15:53, Justin Lemkul wrote:
>>>
>>>>
>>>>
>>>> On 6/19/15 10:52 AM, anu chandra wrote:
>>>>
>>>>> Dear Gromacs users,
>>>>>
>>>>> I am planing to do a protein simulation in acyl chain united-atom POPC
>>>>> membrane model. It will of great help if few of my queries regarding
>>>>> setting up the system get answered.
>>>>>
>>>>> 1. Which force filed will be suitable for united atom (acyl chain)
>>>>> POPC?
>>>>> Will CHARMM36 have united atom force filed for POPC?
>>>>>
>>>>>
>>>> No.  CHARMM36 is an all-atom force field.
>>>>
>>>>  2. can somebody suggest me a site where I can get united atom membrane
>>>>> model of POPC membrane?
>>>>>
>>>>>
>>>> http://wcm.ucalgary.ca/tieleman/downloads
>>>>
>>>>  3. Will CHARMM-gui a good option for build the this particular system?
>>>>>
>>>>>
>>>> Not if you want a united-atom model.
>>>>
>>>> -Justin
>>>>
>>>>
>>>
>>
> --
> Dr Thomas Piggot
> University of Southampton, UK.
>
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