Hi XAvier, Yes, now it makes sense.
Thank you very much for making it clear. 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 8:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_dist The output of g_dist gives: time distance DeltaX DeltaY DeltaZ distance = sqrt(DeltaX**2+DeltaY**2+DeltaZ**2) DeltaX, Y or Z are the differences of the atomic (COM) positions in each direction. A negative value simply means that one of the atoms (COM) has a value larger than the other one in the corresponding direction. The negative value is not a distance yet! Just the difference between the two atoms (COM) positions on one direction. Would that make sense? > 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 > ----------------------------------------------------- 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
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