Dear all,
A system contains a molecule type in form R-(OH)3 (500 molecules). I want to analyze the inter-molecule hydrogen bond among the R-(OH)3 molecules. If I am not wrong, what gmx hbond gives out contains also the intra-molecule hydrogen bonds (the hbond between the OH—O(H) within a molecule) which are not of my interest. So, I would be so thankful if one could let me know how to exclude the intra-molecule hydrogen bonds from the what gmx hbond gives out?
I did this for example by doing this. I created 100 .gro file from trajectory. In each .gro file I use hbond to get index file which has information about index of each hbond, for example
hbond between 7 donor 8 H atoms 9 acceptor
So you have in line something like that
7 8 9
So you must work on this data if you know that in your topology atom index for the first molecule is 1 to for example 30 and the next is for example 31 to 60. You must write a script in awk or python. And this script should work like that
7 8 35 your script should count that
5 6 21 your script shouldn’t count that
1 2 89 toy script should count that
You can modify data instead of
7 8 35
5 6 21
1 2 89
You can delete first column and have
8 35
6 21
2 89
etc
and then you create a condition in your script, for example number from 1 to 30 is the first position in the table and number from 31 to 60 is the second,
so
if both acceptor and donor in the same cell in the table you don’t count them, but you must use own script. I don’t think that we have any option in gromacs for something like that