Dear Sir, Thanks for the prompt reply. I want to analyse the structural and dynamical properties of water in the 1st shell of protein. Using the trjorder command I have obtained the ordered water around the protein within 5A. I would like to know how I could use the trjorder output pdb to selectively analyze the radial distribution (RDF) and the mean squared displacement (MSD) of only the 1st shell water using g_rdf and g_msd.
Thank you On Mon, Mar 3, 2014 at 2:27 PM, Mark Abraham <[email protected]>wrote: > I don't know what you are seeking, a definition of the first shell, or of > "how to analyse." > > Mark > On Mar 3, 2014 6:08 AM, "Venkat Reddy" <[email protected]> wrote: > > > Hello, > > > > I have used the trjorder command to order water around 5 Angstrom radius > of > > a protein. Can anyone suggest how the obtained pdb file can be used to > > analyse the system considering only this first shell of water around the > > protein? > > > > Please help me in this regard. > > > > Thanks > > > > -- > > With Best Wishes > > Venkat Reddy Chirasani > > PhD student > > Laboratory of Computational Biophysics > > Department of Biotechnology > > IIT Madras > > Chennai > > INDIA-600036 > > > > > > > > -- > > With Best Wishes > > Venkat Reddy Chirasani > > PhD student > > Laboratory of Computational Biophysics > > Department of Biotechnology > > IIT Madras > > Chennai > > INDIA-600036 > > -- > > 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]. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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].
