Respected Members,
I have generated md_0_1_noPBC.xtc and other related file using gromacs 5.0 . but I am stuck as md_0_1_noPBC.xtc is not opening with vmd . How to do further analysis?
Dear Manoj
VMD is able to open even a crushed xtc file. What kind of option have you been using? I use the following command: vmd initial.gro prod.xtc
Sir,
I am following this tutorial for analysis
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html
I have generated md_0_1.xtc and md_0_1_noPBC.xtc
I am stuck as when i am uploading md_0_1_noPBC.xtc , the screen is blank
As noted above, you have to load a coordinate file first. An .xtc is just a binary containing box vectors and coordinates. VMD has no knowledge of what the atoms are or how to connect them, so you have to start with a coordinate file and load the trajectory as data for that coordinate file. Do some VMD tutorials; this is covered in the simple examples.
Thank you sir for your valuable suggestions.
I got my results and have also generated final pdb structure using .gro and .xtc file .
Thank you
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