Dear users,
I have a system of protein in solution and I want to make an index file of water molecules present within 5 A of the protein. As simulations go on, the water number as well as the identity change with time. So, I want to make an index file that will be updated in each and every frame. Can anyone suggest me how to do that? Any comments on this topic will be highly appreciated.
Sasthi
(I don't use Gromacs.) Have you tried gmx select?
https://manual.gromacs.org/documentation/current/onlinehelp/gmx-select.html
Dear Martin Klvana ,
I have tried gmx select, but the problem is, I am not sure what should be the proper command from the gmx select in order to get the desired result.
Martin Klvana Thank you for the reply. I have tried the command you suggested, but it fails. The following command I tried:
gmx select -f md_0_100_noPBC.xtc -s md_0_100.tpr -on output.ndx -select group water within 0.5 of group protein -b 95000 -e 100000
The error saying - invalid selection 'group'.
Enclose the selection in double quotes:
-select "group Water within 0.5 of group Protein"
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