[gmx-users] Looking for a Gromacs' tool to find lipid molecules which are located in a shell in the x-y plane around a drug molecule intercalated in a bilayer

[Thomas Piggot]

Hi Seyed,

You might want to take a look at the modified version of g_order (gmx 
order) provided as part of the SI of one of my papers:

https://pubs.acs.org/doi/suppl/10.1021/acs.jctc.7b00643

This code should be able to calculate order parameters at defined radial 
distances around a central object. You can find more details about the 
radial calculation in the work (and SI) of the below paper from Reid Van 
Lehn, who provided most of the modifications to the g_order program 
including this radial calculation:

https://pubs.acs.org/doi/abs/10.1021/jp506239p

I wasn't really interested in this part of the code for what I was doing 
and so you should check for yourself that it is working correctly.

Cheers

Tom

On 31/05/18 11:08, Mark Abraham wrote:
> Hi,
>
> Analysis based on so-called "dynamic selections" need to be done in this
> way - form the selection and then compute based upon it. That can be tricky
> if the selection is constructed in such a way that it does not always have
> the same number of molecules and/or particles. Generally one needs to
> construct the atomic indices (ie. in an index group in an index file) and
> use a tool that matches the selection to a frame, but few of the GROMACS
> tools are (yet) capable of this.
>
> I don't know how order parameters are calculated in order to comment any
> further.
>
> Mark
>
> On Thu, May 31, 2018 at 11:48 AM Seyed Mojtaba Rezaei Sani <
> s.m.rezaeisani at gmail.com> wrote:
>
>> Hi Mark,
>>
>> Thank you for your answer. Actually, to define the shell size I use the
>> distance between the phosphorus of neighboring lipids and the center of
>> mass of the drug. I use gmx select to find phosphorus atoms accommodated in
>> the shell and then manually find the corresponding acyl chains in all four
>> regions (which is not an easy and fast method). Moreover, I am conducting
>> an umbrella sampling simulation with nearly 40 windows. In each window the
>> drug is allowed to move freely in the x-y plane and consequently the
>> locations of regions change spatially which makes the calculation
>> extraordinary difficult for me. Do have any more intelligent idea to do
>> this?
>>
>> On Thu, May 31, 2018 at 12:08 PM, Mark Abraham <mark.j.abraham at gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> gmx select is the tool for making complicated selections. See its
>>> documentation.
>>>
>>> Mark
>>>
>>> On Wed, May 30, 2018 at 2:57 PM Seyed Mojtaba Rezaei Sani <
>>> s.m.rezaeisani at gmail.com> wrote:
>>>
>>>> Dear all,
>>>>
>>>> I am trying to calculate the order parameter of lipid acyl chains in a
>>>> bilayer surrounding a drug molecule using Gromacs. To do this, I
>> defined
>>>> four regions in the bilayer: two local regions within a considered
>> shell
>>> in
>>>> the x-y plane around the drug (one for the leaflet containing the drug
>>> and
>>>> the other for the opposite one) and two global regions beyond the
>> shell.
>>>> My problem is that how to find lipid molecules which are located in the
>>>> local shell in order to make an index group of their carbon chains for
>>>> calculation of order parameter. Is there any Gromacs' tool for such
>>>> calculation?
>>>>
>>>> Best regards,
>>>>
>>>>
>>>> --
>>>> Seyed Mojtaba Rezaei Sani
>>>>
>>>> Institute for Research in Fundamental Sciences (IPM)
>>>> School of Nano-Science
>>>> Shahid Farbin Alley
>>>> Shahid Lavasani st
>>>> P.O. Box 19395-5531
>>>> Tehran, Iran
>>>> Tel: +98 21 2310 <+98%2021%202310> <+98%2021%202310>  (3069)
>>>> --
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>>
>>
>> --
>> Seyed Mojtaba Rezaei Sani
>>
>> Institute for Research in Fundamental Sciences (IPM)
>> School of Nano-Science
>> Shahid Farbin Alley
>> Shahid Lavasani st
>> P.O. Box 19395-5531
>> Tehran, Iran
>> Tel: +98 21 2310 <+98%2021%202310>  (3069)
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
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>>
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>>

-- 
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.