Hi, I have the output files for an MD movie from Gromacs, an xtc and a tpr file. When trying to build the movie, Chimera ask for a tpr and trr files for the Gromacs input. I try anyway with my files but naturally Chimera crashes. Any help for this? Thank you in advance. Alex.
Hi Alex, Sorry -- currently Chimera does not support the xtc trajectory format from Gromacs, only trr: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.ht...
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 11, 2010, at 2:59 PM, Alex Perálvarez Marín wrote:
Hi, I have the output files for an MD movie from Gromacs, an xtc and a tpr file. When trying to build the movie, Chimera ask for a tpr and trr files for the Gromacs input. I try anyway with my files but naturally Chimera crashes. Any help for this? Thank you in advance. Alex.
Hi Alex, As Elaine noted, we only currently support the .trr coordinate files. I have opened a feature-request ticket in our Trac database for xtc support so that you will be notified if I ever have time to implement xtc support. Unfortunately I get very little time to work on MD features for Chimera since we simply do not prioritize it since the feeling is that VMD concentrates on such support and it is a better use of our developer time to work on novel features in other problem domains rather than to duplicate features of VMD. Also, Gromacs formats are typically much harder to add than other formats since they are not documented well enough to implement without actually reading through the relevant Gromacs source code. I know that the .trr format was a bear and took me about 3 days to implement (most formats are about a half day). Looking at the .xtc documentation it also looks like a lot of work due to the extensive use of coding tricks to reduce the file size as much as possible. I'm sorry that I don't have a more encouraging answer for you. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jan 11, 2010, at 2:59 PM, Alex Perálvarez Marín wrote:
Hi,
I have the output files for an MD movie from Gromacs, an xtc and a tpr file. When trying to build the movie, Chimera ask for a tpr and trr files for the Gromacs input. I try anyway with my files but naturally Chimera crashes. Any help for this? Thank you in advance.
Alex. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks for the info. Best, Alex. 2010/1/12 Eric Pettersen <pett@cgl.ucsf.edu>:
Hi Alex, As Elaine noted, we only currently support the .trr coordinate files. I have opened a feature-request ticket in our Trac database for xtc support so that you will be notified if I ever have time to implement xtc support. Unfortunately I get very little time to work on MD features for Chimera since we simply do not prioritize it since the feeling is that VMD concentrates on such support and it is a better use of our developer time to work on novel features in other problem domains rather than to duplicate features of VMD. Also, Gromacs formats are typically much harder to add than other formats since they are not documented well enough to implement without actually reading through the relevant Gromacs source code. I know that the .trr format was a bear and took me about 3 days to implement (most formats are about a half day). Looking at the .xtc documentation it also looks like a lot of work due to the extensive use of coding tricks to reduce the file size as much as possible. I'm sorry that I don't have a more encouraging answer for you. --Eric
Eric Pettersen
UCSF Computer Graphics Lab
On Jan 11, 2010, at 2:59 PM, Alex Perálvarez Marín wrote:
Hi,
I have the output files for an MD movie from Gromacs, an xtc and a tpr file. When trying to build the movie, Chimera ask for a tpr and trr files for the Gromacs input. I try anyway with my files but naturally Chimera crashes. Any help for this? Thank you in advance.
Alex. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
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Alex Perálvarez Marín -
Alex Perálvarez Marín -
Elaine Meng -
Eric Pettersen