Hi all,
I am trying to make a movie from a MD simulation using Chimera 1.12. This time I am facing problems because the .xtc file is too large (above Gb) and my computer freezes. If I use a 'corrected and reduced' .xtc file (without solvent and ion molecules and well bellow 100 Mb) there is an inconsistency in the number of atoms with the original .tpr file thus the trajectory can not visualized.
I guess I can reduce the .xtc file by reducing the timesteps/frames but is there any way to reduce/modify a .tpr file? If I am not wrong this can not be accomplish using trjconv nor convert-tpr commands...
Regards,
Xabi
Xabier Arias I don't use Chimera. I use VMD, but you might be able to load a *.pdb or *.gro file of your system's topology into Chimera instead of loading the *.tpr. That's what I always do for VMD.
To get a *.pdb / *.gro file of your system without solvent and ions, you'll need an index.ndx file with a group corresponding to that description. It sounds like you already have one if you created an *.xtc without solvent or ions (presumably, with gmx trjconv). Then you can also use the "gmx trjconv" with the " -dump" flag to print a *.gro file of your topology at whichever frame of the trajectory you like. Units default to picoseconds if you want a specific frame (e.g -dump 1000, to print the frame closest to 1 ns). I suspect you might be able to make a movie by then loading the trajectory's frames for that *.pdb/*.gro. That's what I always do in VMD.
Hope that helps, if you want more info, see here: http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-trjconv.html
JD Tamucci Thnaks for the comment and sorry for my late reply! I´d rather prefer to use Chimera for this purpose cause the movies look better (or that´s what I think). Unfortunately, and as far as I know there is no way to use the coordinate files (.gro, .pdb) as a substitute of the .tpr file!!!
I am replying myself because I have come with one solution. It is faster to create a new .tpr file without the solvate and ions as following: it is very convenient to create a new em1.tpr file using the -c box.gro file and the -p topol.top file as arguments. Of note the ions and solvent molecules from this top.topol file have to be previously deleted.
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