On Fri, Jul 15, 2011 at 1:41 PM, Mark Abraham <[email protected]>wrote:
> ** > On 15/07/2011 7:31 PM, Martin Kamp Jensen wrote: > > Hello, > > I am trying to evaluate energy values of several conformations using a > (pseudo)trajectory. Currently, I am concatenating GROMOS-96 files (.g96) and > using that as a trajectory. For some reason the second conformation in a > trajectory is ignored. So e.g. if I have three conformations (1.g96, 2.g96, > and 3.g96), then concatenate them into 1+2+3.g96, and then use the latter > file as a trajectory, the conformation of 2.g96 is ignored when using mdrun > -rerun with a suitable binary run file. > > I have created an archive [1] with files demonstrating the problem. Use > the "run" script for a stepwise demonstration of the problem: The output of > mdrun shows that the last frame processed is one less then expected for > concatenated files. Further, it is the second frame that is missing which > can be determined by looking at the energy values in the energy file > generated by mdrun. > > I have no clue what is going on here. I hope someone can provide some > insights. (The same approach seems to work fine with PDB files instead of > GROMOS-96 files, but there is less precision in PDB files and because of > some irrelevant details it is easier for me to work with GROMOS-96 files at > the moment.) > > [1] http://dl.dropbox.com/u/2666968/GROMACS/missingframe.tar > > Thanks, > Martin. > > > That's a bug. Reading the .g96 file format as a trajectory uses some dirty > dirty non-thread-safe code, and the cleanup a few years ago to make things > thread-safe did that without preserving correct functionality. I suggest you > concatenate separate .g96 files using trjcat into .trr format, and use rerun > on that. > Too bad, but thank you for explaining. Is your suggestion based on the fact that the functionality is completely unreliable? I mean, if the bugs are known (e.g. 2nd frame is always ignored), it would maybe be better to just work around them. (It would be a bit sad to write out 100 or 1000 g96 files and then use trjcat since I will need to do that millions of times during a run of my application.) Regards, Martin. > > Mark > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
