Hi Tushar Ranjan Moharana, g_select (or gmx select if using gromacs version >5) will let you make an index file for each frame then you just have to loop through the index file and report the distances. You would make a selection like (you'll need to double check to make sure this is an accurate selection)
group "Methanol" and within 0.4 of group "Protein" This will generate an index file that has the all of the methanol molecules within 0.nm4 of the protein at each time step as different groups. You should be able to write a script from there that will give you the average distance. -Micholas =================== Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________________ From: [email protected] <[email protected]> on behalf of Tushar Ranjan Moharana <[email protected]> Sent: Tuesday, September 01, 2015 5:15 AM To: [email protected] Subject: [gmx-users] Analyze neighbors of a residue within a cutoff distance during simulation Hi Everyone, I have simulated a protein in 40 % methanol. Now I want to analyze the average distance between any amino acid and all the methanol molecule which comes to close to (less than 0.4 nm) that amino acid during the simulation. I tried many GROMACS analysis tool for this but I couldn't succeed. Can anybody kindly suggest me which analysis tool will be useful for me. Thanks a lot in advance. "A society with free knowledge is better than a society with free food" Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
