I have performed MD simulation with RNA (3 strand helix) using GROMACS. During MD-run the strands are separated due to PBC and also broken during PBC. How to "unwrap" or make the molecule intact?
Is it possible to do something like "wrap all off" in GROMACS, as is done in NAMD?
If it is only for display purpose, you can do it in VMD.
pbc wrap -compound fragment
Hi Angana,
you can use command
gmx trjconv -s md.tpr -f traj_comp.xtc -pbc nojump -o traj_nojump.xtc
use gmx trjconv -h to know all other parameters you need to add like
1. traj.xtc
2. md.tpr
3. index.ndx
to overcome PBC error.
regards
Tanuj
Gaurav and Tanuj,
Thank you for replying. I have tried these two ways but did not get success. I am uploading the necessary files and a chunk of my trajectory file (containing RNA only). If possible kindly have a look and let me know if anything can be done.
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