Dear all,
Happy Christmas!
I ran molecular dynamics of protein-ligand complex using gromacs. Unfortunately, when I visualized in PyMol, I found something odd. I attached here two photographs. If anybody knows that what has been happened to this MD then please share your comments. Thank you
Hi Shravan B Rathod ,
I believe you need to do some recentering of your protein.
If you were using GROMACS, you can use the "gmx trjconv" command.
Dear Farrah Wahidah Ridzwan,
Thank you for your quick comment. I highly appreciate your response.
Yes, I use Gromacs. It would be better if you tell that on which MD file (is it on .XTC MD file?) "gmx trjconv" should I run this command and how?
Thanks
I usually use this commands:
gmx trjconv -f md.xtc -s md.tpr -o md2.xtc -pbc cluster -n index.ndx
gmx trjconv -f md2.xtc -s md.tpr -o md3.xtc -pbc mol -ur compact -center -n index.ndx
For both, I will select the complex for the first option and the system for the next.
Of course it all depends on your preferences.
You can try "-pbc nojump" too.
You can refer all of the available options for "gmx trjconv" here: https://manual.gromacs.org/documentation/2019/onlinehelp/gmx-trjconv.html
Hope this helps. All the best
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