Dear friends,
I have a problem with gromacs.
My protein rotates in md simulations.
I run the simulation in 300K but the protein rotates and suddenly starts doing weird things! It completely unfolds and starts jumping!
What do you recommend me to do?
Thank you!
There is nothing wrong about the rotation (unless the rotation is too fast). As to the protein stability, you would need to check the structure and atom-type attribution. Also, the protein might needs ions at specific locations to maintain its fold. So, you would need to check if this is the case for your protein of interest and not remove those ions while preparing the structure for MD.
Hi! With "start jumping", I suppose you are dealing with PBC. In this case, I think it is a problem of visualisation. Have you tried to submit your trajectory to a trj_conv run?
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Hi,
Try converting trajectory by trjconv:
gmx trjconv -pbc whole -center
In case you have multiple chains, use -cluster option to keep relative position of the protein:
gmx trjconv -pbc cluster -center
Good luck!
Sincerely,
ALexandr
Thanks to all of my friends!
Giuseppina,
Yes! I am dealing with pbc box!
I am trying this commands, I will let you know the result.
Best,
Unfortunately it did not work!
The problem is that,
I am working in pbc, but when I open my .gro and .xtc files in vmd, after 100ns the protein starts to rotate badly and gets crazy actually! It rotates and jumps and runs everywhere!
Things will not get better until you convert the original xtc file into a new one, which would have pbc jumps fixed and protein structures aligned to a reference frame.
This command would fix the pbc issue and write corrected frames to protein-md-nojump.xtc:
trjconv -s protein.tpr -f protein-md-input.xtc -o protein-md-nojump.xtc -pbc nojump -dt 10
0
This command would align structures from protein-md-nojump.xtc to the initial protein structure and write the output to protein-md-output.pdb:
trjconv -s protein.tpr -f protein-md-nojump.xtc -o protein-md-output.pdb -fit rot+trans
3,0
Use protein-md-output.pdb for your VMD analysis.
you need to do several consecutive PBC treatments using trjconv. For example, 1. -pbc nojump. 2. -pbc mol -ur compact; 3. -pbc center (specific group) and 4. -pbc whole ... etc.
Good luck.
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