Thanks Justin for the help. But if I want to look the dipole auto correlation or hydrogen bond dynamics ... is that possible?
On Fri, Feb 28, 2014 at 4:38 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/28/14, 5:38 AM, abhijit Kayal wrote: > >> Dear Gromacs users, >> >> My system contained CNT+ water. I have created a dynamically >> index.ndx file >> which contain the number of water molecules in each frame inside cnt. >> Now I want to study the dipole orientation of these water molecules. But I >> can't select all the groups at a time. From the mailing lists search I >> came >> to know that any gromacs analysis tools can't do this. So is there any >> other way to do these type of analysis. I am using gromacs 4.5.5. >> >> > You have to analyze each frame individually rather than processing the > trajectory in one pass. With a simple shell script, you can loop through > the index groups, write out a corresponding frame from the trajectory, then > analyze it. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > > -- > 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 gmx-users-requ...@gromacs.org. > -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- 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 gmx-users-requ...@gromacs.org.
