[gmx-users] Help required for calculation of protein coverage % wrt time

Sarath Chandra sarathchandradantu at gmail.com
Thu May 19 15:10:46 CEST 2016

You can use g_contacts tool which will give you list of residues which are
in contact with the membrane and their frequencies. You might have to write
an overhead script to convert the residues in contact to %Protein in contact




Sarath Chandra Dantu, PhD, ELS
Room No. 606, New BSBE Building
Department of Biosciences and Bioengineering
Indian Institute of Technology Bombay
Powai Mumbai, 400-076, India

On 19 May 2016 at 18:35, Antara mazumdar <antara.mazumdar at igib.in> wrote:

> Dear gromacs users,
> I have a peripheral membrane protein which I have simulated using Charmm 36
> in a mixed lipids bilayer. I want to calculate the percentage of protein in
> contact with membrane wrt time. I already have residue wise distances from
> membrane calculated.
> Can anyone suggest me how to go about it after this?
> Antara Mazumdar
> Core Committee Member
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