Re: [gmx-users] pair distribution function

[Archana Sonawani-Jagtap]

Thank you.


On Sun, Oct 6, 2013 at 8:12 PM, Justin Lemkul  wrote:

>
>
> On 10/6/13 10:36 AM, Archana Sonawani-Jagtap wrote:
>
>> I have simulations for different peptides in POPC bilayer.
>>
>> I want to calculate pair distribution function (pdf) between negatively
>> charged phosphate residue of POPC and positively charged residues of
>> peptide. Is there any tool available in gromacs for plotting these values?
>>
>>
> The closest you can get with a built-in Gromacs program is a radial
> distribution function with g_rdf.
>
>
>  Secondly, how to calculate the center of mass for a bilayer?
>>
>>
> g_traj -ox -com
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  |
> (410) 706-7441
>
> ==**
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-- 
Archana Sonawani-Jagtap
Senior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339
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Re: [gmx-users] pair distribution function

[Justin Lemkul]

On 10/6/13 10:36 AM, Archana Sonawani-Jagtap wrote:

I have simulations for different peptides in POPC bilayer.

I want to calculate pair distribution function (pdf) between negatively
charged phosphate residue of POPC and positively charged residues of
peptide. Is there any tool available in gromacs for plotting these values?



The closest you can get with a built-in Gromacs program is a radial distribution 
function with g_rdf.



Secondly, how to calculate the center of mass for a bilayer?



g_traj -ox -com

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] pair distribution function

[Archana Sonawani-Jagtap]

I have simulations for different peptides in POPC bilayer.

I want to calculate pair distribution function (pdf) between negatively
charged phosphate residue of POPC and positively charged residues of
peptide. Is there any tool available in gromacs for plotting these values?

Secondly, how to calculate the center of mass for a bilayer?

Any help is highly appreciated.

-- 
Archana Sonawani-Jagtap
Senior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339
-- 
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/Search before posting!
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