Hi, I would like to keep only the water molecules in the first hydration shell for visualization purpose. Using trjorder I could successfully create the ordered trajectory. But I could not follow the following statement in the manual:
"When an index group of the first n waters is made, the ordered trajectory can be used ...." How do I create this index file? Will the following entry work? [ Hydration Shell ] 1 2 3 .... n Of course I'll put integers till n. Next can I use trjconv to keep only the protein along with these n water molecules in the trajectory? Possibly I am asking a very naive question, but I could not find a general guideline to write the index file in the manual. Thanks and regards, Suman Chakrabarty. _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
