On Wed, Sep 28, 2011 at 1:33 AM, Mark Abraham <[email protected]>wrote:
> On 28/09/2011 9:11 AM, Martin Kamp Jensen wrote: > > On Tue, Sep 27, 2011 at 3:09 PM, Justin A. Lemkul <[email protected]> wrote: > >> >> >> Martin Kamp Jensen wrote: >> >>> Hello, >>> >>> I need to combine several trajectories (.xtc) and energy file (.edr) >>> pairs. In the end I need all the conformations of the trajectories and a >>> specific energy value for each of them. >>> >>> To combine two trajectories, I use trjcat [1] like this: >>> >>> trjcat -f first.xtc second.xtc -o combined.xtc -cat >>> >>> >>> Since I just need the conformations (the coordinates) and I do not care >>> about "step" and "time," I guess this is okay. >>> >>> To combine two energy files, it seems like I should use eneconv [2]. >>> Unfortunately, there is not an argument like "-cat" for trjcat, which means >>> that the tool will not include all energies from the input files in the >>> output file ("In case of double time frames the one in the later file is >>> used."). I should probably note that I do not need "Av. Energy" or "Sum >>> Energy," I just need the energy frames in the energy files concatenated so >>> that I can easily extract them and assign them to the correct conformations. >>> >>> Any ideas? >>> >>> >> Don't use the -cat option of trjcat. Normally you'll have duplicate time >> frames, for instance, in the final frame of "first.xtc" and the first frame >> of "second.xtc." If they are the same, you do not need to keep them. The >> -cat option, as I understand it, is basically for fudging different >> trajectories together for non-standard purposes. If you omit -cat then >> you'll have .edr and .xtc files that match. >> > > But my purposes are non-standard and I need all of the conformations of > both (or more) input trajectories as well as the corresponding energy > frames. I see that, per the description of "-cat," time and step information > will be messed up, but that is not a problem. > > > So pre-process with -settime such that duplicate times cannot arise. > Ah, thanks! > > Mark > > > > (I have created a program that reads conformations from a trajectory and > assigns a specific energy value from a corresponding energy file to each of > the conformations. I just had a special case where I was asked to work with > several trajectories and energy files which were provided to me and it would > be nice to just concatenate them and then not introduce special > functionality in my program to handle it.) > > >> >> -Justin >> >> >> Regards, >>> Martin. >>> >>> [1] http://manual.gromacs.org/online/trjcat.html >>> [2] http://manual.gromacs.org/online/eneconv.html >>> >>> >> -- >> ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- >> 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 >
-- 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
