> >> [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) > > > > I see something similar with my own CG trajectories. I do not routinely > inspect > them; I typically rely on the energy curve and final output structure to > determine the adequacy of the procedure. > > What I find in my own case is that the third decimal differs by no more than > 1 > unit between the reference structure and the constituent frames of the .trr > file. It would seem to me that if you are seeing no difference along the > different frames, this is probably just a machine precision issue. > > Differences are more obvious, however, when using steepest descents, and the > trajectory, when viewed in VMD, shows continual change in the structure. > > >> 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 would think that 0.1 nm is somewhat large for a simple minimization > procedure, > although this is probably dependent upon system size and which components you > are analyzing. > > -Justin > > >>> 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
I found the likely cause in the source and have submitted a bug report (# 321). My impression is that the minimization itself is not affected. -Heiko __________________________________________________________________________ Verschicken Sie SMS direkt vom Postfach aus - in alle deutschen und viele ausländische Netze zum gleichen Preis! https://produkte.web.de/webde_sms/sms _______________________________________________ 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
