Dear Mark, Thanks for your suggestion! It works now! Xujun ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark Abraham [mark.j.abra...@gmail.com] Sent: Wednesday, April 08, 2015 10:46 To: Discussion list for GROMACS users Subject: Re: [gmx-users] command line with gmx_mpi gangle for choosing the vector formed by coms of two planes
On Wed, Apr 8, 2015 at 10:33 AM, LIANG Xujun <xujun.li...@cea.fr> wrote: > Hello all, > > I have one question: > > I would like to compute the angle between the normal vector of plane 1 and > the com vector of plane 1 and plane 2 using gmx_mpi gangle (version 5.0.4). > The command is as follows: > > gmx_mpi gangle -f ....xtc -s ....tpr -n ....ndx -g1 plane -group1 -g2 > vector -group2 -oav test_angle_vector.xvg -b .. -e ... > > After enter the above command, I need to make the following choices: > 0- <enter>-<ctrl-D>-com of group 0 plus com of group 1-<enter>-<ctrl-D> > > For automatically analyzing, I wrote the above choice into a text > file----echo -e "0\r com of group 0 plus com of group 1\r", unfortunately, > it doesn't work. > Probably \r is not sufficient, follow http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts. But I understand that it t is intended that you pass selection strings directly to -group1 and -group2 (see gmx gangle -h) so doing that might work better. Mark > Could you please tell me how can I achieve the above goal? > > Thanks for your help in advance! > > Xujun > -- > 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. > -- 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. -- 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.