Re: [gmx-users] calculate area per lipid and bilayer thickness versus time

[Kieu Thu Nguyen]

Thank Justin so much ! Sorry about my stupid question. I have looked the
algorithm and i got it.


On Tue, Jan 22, 2013 at 8:05 PM, Justin Lemkul  wrote:

>
>
> On 1/22/13 12:00 AM, Kieu Thu Nguyen wrote:
>
>> Thank Justin ! And i used GridMAT-MD as you advised.
>>
>> I got result "The average bilayer "thickness" will be printed to
>> 50x50_average_pbc.dat". But that result is only equal to a half of
>> experiment result. I think "bilayer thickness" is equal to the sum of "top
>> leaflet thickness" and "bottom leaflet thickness". So should i double "The
>> average bilayer "thickness"..." mentioned above ?
>>
>>
> No.  The program measures the total thickness, using the reference atoms
> you provide.  The individual files ("top thickness" and "bottom thickness")
> represent two ways of measuring the same thing, using both leaflets as
> reference, which are then averaged to produce the desired distance file.
>  Please refer to our paper for the algorithm.
>
>
>  And i do not get average area per lipd, just "The average area per lipid
>> in
>> the top leaflet is 64.2329395973154 sq. Angstroms. The average area per
>> lipid in the bottom leaflet is 63.3821721854305 sq. Angstroms".
>>
>>
> The data file contains areas for each individual lipid, which can be
> averaged.
>
> -Justin
>
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
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Re: [gmx-users] calculate area per lipid and bilayer thickness versus time

[Justin Lemkul]

On 1/22/13 12:00 AM, Kieu Thu Nguyen wrote:

Thank Justin ! And i used GridMAT-MD as you advised.

I got result "The average bilayer "thickness" will be printed to
50x50_average_pbc.dat". But that result is only equal to a half of
experiment result. I think "bilayer thickness" is equal to the sum of "top
leaflet thickness" and "bottom leaflet thickness". So should i double "The
average bilayer "thickness"..." mentioned above ?



No.  The program measures the total thickness, using the reference atoms you 
provide.  The individual files ("top thickness" and "bottom thickness") 
represent two ways of measuring the same thing, using both leaflets as 
reference, which are then averaged to produce the desired distance file.  Please 
refer to our paper for the algorithm.



And i do not get average area per lipd, just "The average area per lipid in
the top leaflet is 64.2329395973154 sq. Angstroms. The average area per
lipid in the bottom leaflet is 63.3821721854305 sq. Angstroms".



The data file contains areas for each individual lipid, which can be averaged.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] calculate area per lipid and bilayer thickness versus time

[Kieu Thu Nguyen]

Thank Justin ! And i used GridMAT-MD as you advised.

I got result "The average bilayer "thickness" will be printed to
50x50_average_pbc.dat". But that result is only equal to a half of
experiment result. I think "bilayer thickness" is equal to the sum of "top
leaflet thickness" and "bottom leaflet thickness". So should i double "The
average bilayer "thickness"..." mentioned above ?

And i do not get average area per lipd, just "The average area per lipid in
the top leaflet is 64.2329395973154 sq. Angstroms. The average area per
lipid in the bottom leaflet is 63.3821721854305 sq. Angstroms".

Thanks in advance !
KT


On Mon, Jan 21, 2013 at 11:03 PM, Justin Lemkul  wrote:

>
>
> On 1/21/13 10:17 AM, Kieu Thu Nguyen wrote:
>
>> Thank Justin ! That is APL. How about bilayer thickness ? I made
>> density.xvg file of headgroup from using g_density.
>>
>>
> g_dist with index groups specifying however you want to define the
> boundaries for the membrane, or (shameless plug) a lateral projection of
> thickness (from which an average can easily be derived:
> http://bevanlab.biochem.vt.**edu/GridMAT-MD/
> .
>
> -Justin
>
>
>> On Mon, Jan 21, 2013 at 7:31 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 1/21/13 5:12 AM, Kieu Thu Nguyen wrote:
>>>
>>>  Dear All,

 I want to know that my lipid bilayer is equilibrated or not yet. So i
 want
 to calculate the change of area per lipid and the bilayer thickness
 versus
 time.

 Which tool or method should i use ?


  Extract box vectors over time from the .edr file, then use a script of
>>> your own creation to multiply them and divide by the number of lipids per
>>> leaflet.  Of course, that goes out the window if there is a protein
>>> present.
>>>
>>> -Justin
>>>
>>> --
>>> ====
>>>
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> >
>>>
>>> ====
>>>
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> >
>>> * Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Search>> Mailing_Lists/Search>before
>>> posting!
>>>
>>> * Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-requ...@gromacs.org.
>>> * Can't post? Read 
>>> http://www.gromacs.org/Support/Mailing_Lists
>>> 
>>> >
>>>
>>>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
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Re: [gmx-users] calculate area per lipid and bilayer thickness versus time

[Justin Lemkul]

On 1/21/13 10:17 AM, Kieu Thu Nguyen wrote:

Thank Justin ! That is APL. How about bilayer thickness ? I made
density.xvg file of headgroup from using g_density.



g_dist with index groups specifying however you want to define the boundaries 
for the membrane, or (shameless plug) a lateral projection of thickness (from 
which an average can easily be derived: http://bevanlab.biochem.vt.edu/GridMAT-MD/.


-Justin



On Mon, Jan 21, 2013 at 7:31 PM, Justin Lemkul  wrote:




On 1/21/13 5:12 AM, Kieu Thu Nguyen wrote:


Dear All,

I want to know that my lipid bilayer is equilibrated or not yet. So i want
to calculate the change of area per lipid and the bilayer thickness versus
time.

Which tool or method should i use ?



Extract box vectors over time from the .edr file, then use a script of
your own creation to multiply them and divide by the number of lipids per
leaflet.  Of course, that goes out the window if there is a protein present.

-Justin

--
==**==

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin

==**==
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 posting!
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--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] calculate area per lipid and bilayer thickness versus time

[Kieu Thu Nguyen]

Thank Justin ! That is APL. How about bilayer thickness ? I made
density.xvg file of headgroup from using g_density.


On Mon, Jan 21, 2013 at 7:31 PM, Justin Lemkul  wrote:

>
>
> On 1/21/13 5:12 AM, Kieu Thu Nguyen wrote:
>
>> Dear All,
>>
>> I want to know that my lipid bilayer is equilibrated or not yet. So i want
>> to calculate the change of area per lipid and the bilayer thickness versus
>> time.
>>
>> Which tool or method should i use ?
>>
>>
> Extract box vectors over time from the .edr file, then use a script of
> your own creation to multiply them and divide by the number of lipids per
> leaflet.  Of course, that goes out the window if there is a protein present.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
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Re: [gmx-users] calculate area per lipid and bilayer thickness versus time

[Justin Lemkul]

On 1/21/13 5:12 AM, Kieu Thu Nguyen wrote:

Dear All,

I want to know that my lipid bilayer is equilibrated or not yet. So i want
to calculate the change of area per lipid and the bilayer thickness versus
time.

Which tool or method should i use ?



Extract box vectors over time from the .edr file, then use a script of your own 
creation to multiply them and divide by the number of lipids per leaflet.  Of 
course, that goes out the window if there is a protein present.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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