hi XAvier, Thanks for your response. It was a question more of about how you would interpret the negative values(distance) in a particular component.
With thanks, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -----Original Message----- From: [EMAIL PROTECTED] on behalf of Xavier Periole Sent: Tue 25/09/2007 10:13 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_dist On Tue, 25 Sep 2007 10:03:30 +0100 "Naser, Md Abu" <[EMAIL PROTECTED]> wrote: > Hi David, > > Yes, it should be a vector as it is a difference between the center of mass >of two groups in > x,y, and z directions. Then, negative means an opposite direction. Is that >right? g_dist gives the distance and the component in each direction. The components been the difference between the atomic (or COM) positions there is no problem in having a negative value. > > Abu Naser > > School Of Life Sciences > Heriot-Watt University > Edinburgh EH14 4AS > Email: [EMAIL PROTECTED] > Phone: +44(0)1314518265 >Fax : +44(0) 131 451 3009 > > > > > > > -----Original Message----- >From: [EMAIL PROTECTED] on behalf of David van der Spoel > Sent: Tue 25/09/2007 9:42 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] g_dist > > Naser, Md Abu wrote: >> >> >> Hi all user, >> >> I have just calculated a distance between backbone and side chain of the >> same protein. I get >> negative distance along x and y direction. What dose negative distance mean? >> > please be more specific. is that a vector? > >> Thanks in advance. >> >> >> Abu Naser >> >> School Of Life Sciences >> Heriot-Watt University >> Edinburgh EH14 4AS >> Email: [EMAIL PROTECTED] >> Phone: +44(0)1314518265 >> Fax : +44(0) 131 451 3009 >> >> >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> 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 > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 > ----------------------------------------------------- XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole ----------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
