> -----Ursprüngliche Nachricht----- > Von: "Justin A. Lemkul" <[email protected]> > Gesendet: 01.05.09 03:10:01 > An: Discussion list for GROMACS users <[email protected]> > Betreff: Re: [gmx-users] configuration does not change in minimization > trajectory
> > > [email protected] wrote: > > Hello all, > > > > I am doing a cg minimization with Gromacs-4.0.3. > > It is compiled on a Linux system with gcc 3.4.6 > > > > All frames in the trajectory are identical to the starting configuration, > > except for the final one, which is clearly different. > > > > How are you assessing this? External viewing programs don't always show the > necessary level of detail. If you use trjconv -dump to drop out a few select > frames, and diff the resulting .gro files, are they indeed identical, or are > there small differences? > All configurations but the last one are strictly identical to the first. (Determined as suggested, using diff on .gro files dumped from the trajectory) > How different is the final structure? Is there a drastic change? Or is it > just > that the change relative to the input structure is more obvious? > The rmsd between the first and last structures is about 0.1 nm, using -nomw with g_rms. So any changes to the structure are local, but obvious in VMD. > > I get the expected number of frames in the trajectory (.trr), > > and the energy saved in the .edr is decreasing. > > But apparently the changes in the structure do not reach the trajectory > > file. > > > > If the energy is changing, then so too should the structure. > I agree, internally the structure must be changing, only the output does not show it. > -Justin > > > Any suggestions? > > > > Heiko > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Thanks for your input, Heiko ____________________________________________________________________ Psssst! Schon vom neuen WEB.DE MultiMessenger gehört? Der kann`s mit allen: http://www.produkte.web.de/messenger/?did=3123 _______________________________________________ gmx-users mailing list [email protected] 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
