[gmx-users] CH3 group and units of POPC?

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 30 11:54:40 CEST 2008

sudheer babu wrote:
> Hi all,
> I want to ask two questions
> 1.I am interested to calculate electron density of -CH3 group of popc 
> bilayer, Is it require to consider (CH3)3 surround by N  and CH3 at 
> tails also or consider CH3 at tails only?

That depends entirely upon what you are looking to examine.  Do you want the 
density at the innermost point in the bilayer, or a combination of all -CH3 
groups in the system?

> 2. I have calculated electron density of PO4, water, N(CH3)3 groups of 
> popc, gromacs calculated the density values in  units of  kg/m\S3\N, but 
> in literature the values in the units (atoms/nm3), Can I plot directly 
> the values with kg/m\S3\N or  have I converted this to nm3 ?

You can make the transformation if you like; the other common representation of 
density that I often see is electron density, which g_density will give you if 
you provide a proper electrons.dat file.


> Could you clear me regarding this questions
> Thanks in advance for help.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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