[gmx-users] help required in plotting percentage of protein in contact with membrane vs time
Antara mazumdar
antara.mazumdar at igib.in
Sat May 21 14:54:31 CEST 2016
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
--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi - 110020
M : +91-9717970040
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