Hi Kay, How about using trjconv to remove periodicity ...then take the modified trajectory and feed it into g_dist? I think this could be a possible solution...... I'd appreciate it, if the hard working and ever resourceful users/developers can inform us whether this is a possible option??... i.e. Would the *tpr file that contains the run parameters cause a conflict??? Best wishes Kia > ------------------------------ > > Message: 7 > Date: Mon, 22 May 2006 18:11:19 +0200 > From: Kay Gottschalk > Subject: Re: [gmx-users] g_dist > To: Discussion list for GROMACS users > Message-ID: > <9722BE5E-C23A-4119-85A7-C23F7DFC7337@physik.uni-muenchen.de> > Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed > > They are not interacting. The distance is larger than 40 Å. But > still,if the distance to the mirror image is 41 Å and to the same > protein in the box is 45 Å, the distance to the mirror image will be > plotted... We are indeed pulling on z. > Best, Kay. > > On May 22, 2006, at 6:02 PM, Xavier Periole wrote: > > > Kay Gottschalk wrote: > > > >> Hi there, > >> > >> we are doing a pulling simulation and want to monitor the > >> distance between two atoms during pulling. Using g_dist the > >> distance is calculated between all mirror images of the periodic > >> boundary conditions, and the minimal distance is calculated. In > >> our case, this is uncomfortable, since the distance should be > >> monotonically increasing, but since after approximately half of > >> the simulation one atoms starts to become closer to the mirror > >> image in the next box, it looks as if the distance is decreasing. > >> Is it possible to switch off the pbc condition in g_dist? I > >> didn't find it in the manual or the user list. > > > > Is it any good to have your two atoms interacting through the > > images ?? > > It does not sound too good to me ... > > > > You can just plot the distance and the size of the box (g_energy > > give the box size) and > > then just substract the corresponding dimension if the box to the > > distance you > > obtained with g_dist. I guess your are pulling on one of the axes !!! > > > > XAvier > > > > -- > > ---------------------------------- > > Xavier Periole - Ph.D. > > > > Dept. of Biophysical Chemistry / MD Group Univ. of Groningen > > Nijenborgh 4 > > 9747 AG Groningen > > The Netherlands > > Tel: +31-503634329 > > Fax: +31-503634398 > > email: x.periole@rug.nl > > web-page: http://md.chem.rug.nl/~periole > > ---------------------------------- > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to gmx-users-request@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Dr. Kay-Eberhard Gottschalk > Applied Physics and Center for Nano Sciences > Ludwig-Maximilians University > Amalienstr. 54 > 80799 Munich, Germany > > Phone: +49-89-2180 3436 > > > > > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > > > End of gmx-users Digest, Vol 25, Issue 84 > ***************************************** > -- Kia Balali-Mood PhD, CBiol, MIBiol Postdoctoral Research Associate, Department of Biochemistry, Oxford University, OX1 3QU, UK sansom.biop.ox.ac.uk/kia/ , tel. +44 (0)1865 275 (380 or 275)