[gmx-users] Extracting trajectory

[anupama sharma]

Dear users,
I want to extract the trajectory of water molecules near the protein
surface within 5 angstorm region. I was able to do that in using gmx select
and gmx trjcat, but it is for only one time frame and than the water
molecules diffuses away for the next time frame. I want to extract the
trajectory of only those water molecules that are near protein surface
within 5 angstorm region for each individual time frame so that i can get
the complete trajectory of water molecules that are near the protein
surface excluding the water molecules that diffuses away in each next
frame......
I will be thankful for help.




Thanks and regards,
Anupama