[gmx-users] help required in plotting percentage of protein in contact with membrane vs time

[Antara mazumdar]

Dear Gromacs users,

  I have a membrane protein simulation performed with gromacs 4.6. I have
calculated the minimum distance of protein residues from upper leaflet of
the lipid bilayer. I also have the time wise atom pair contacts as an
output.
The following command i used :

g_mindist -f SYSTEM_FIT_SIM4_DT100.xtc -s MD_4_NOWATER.tpr -n ../index.ndx
-d 0.7 -o atompair -on numcontact -od mindist.xvg

The atom pair out output i got was as follow :

.000000e+00          2412        281928
1.000000e+02          1630        266151
2.000000e+02          1630        266151
3.000000e+02          2410        284225
4.000000e+02          2412        284225
5.000000e+02          2412        284225
6.000000e+02          2410        284225
7.000000e+02          2410        284225
8.000000e+02          2410        284225
9.000000e+02          2410        284225
1.000000e+03          2405        284225
1.100000e+03          2411        281928
1.200000e+03          2412        284225
1.300000e+03          2332        285163
1.400000e+03          2411        284225
1.500000e+03          2410        284225
1.600000e+03          1555        264261
1.700000e+03          1555        264261
1.800000e+03          1555        264261
1.900000e+03          1554        266958
2.000000e+03          2389        266958
2.100000e+03          2411        285163
2.200000e+03          2412        285163
2.300000e+03          2412        285163
2.400000e+03          2410        285163
2.500000e+03          2410        285163
2.600000e+03          2412        285163


 I now need to find out time wise percentage of protein covering the
membrane. I want to know for instance, at time t=0ns, what is the protein
coverage % and similarly for the entire trajectory i want to calculate this.


Kindly suggest something!!

Kind Regards,
Antara

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CSIR-Institute of Genomics & Integrative Biology
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