I have following doubts in Gromacs ,and want to know if these things are normal? or i am doing something wrong?
1) The protein is outside the solv box ( picture 1).
2) while i am running simulation of protein-ligand complex, md run shows "protein in water" (picture 2)?
1) VMD may visualises the protein outside of the solute box, but this doesn't mean it is outside the unit cell, as there is no 'outside'. I imagine you are using 3D periodic boundary conditions, which are specified in you .mdp file you used during grompp. This allows a molecule to cross the unit cell boundary and reappear on the reverse side. VMD simply keeps molecular together for the sake of visualisation.
Providing your unit cell is large enough such that short-range interactions e.g., LJ/VdW do not 'detect' the same protein as it crosses the unit cell, this is a means of setting up an 'infinite' water environment for your protein to simulate within.
Take a look here:
https://en.wikipedia.org/wiki/Periodic_boundary_conditions
And here, notice that your first concern has been highlighted in the list given:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
2) "Protein in water" is just a title given to one of your files (I think the header in the .gro file but I might be wrong) - it actually means nothing at all.
1) VMD may visualises the protein outside of the solute box, but this doesn't mean it is outside the unit cell, as there is no 'outside'. I imagine you are using 3D periodic boundary conditions, which are specified in you .mdp file you used during grompp. This allows a molecule to cross the unit cell boundary and reappear on the reverse side. VMD simply keeps molecular together for the sake of visualisation.
Providing your unit cell is large enough such that short-range interactions e.g., LJ/VdW do not 'detect' the same protein as it crosses the unit cell, this is a means of setting up an 'infinite' water environment for your protein to simulate within.
Take a look here:
https://en.wikipedia.org/wiki/Periodic_boundary_conditions
And here, notice that your first concern has been highlighted in the list given:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
2) "Protein in water" is just a title given to one of your files (I think the header in the .gro file but I might be wrong) - it actually means nothing at all.
do a trjconv with pbc = mol or nojump option, to have the protein centred in the box
You can check your box boundary by going VMD -----> extensions -----> Tk console
type PBC box
check the box properly
It's PBC problem. you can overcome this by typing following commad
trjconv -f xx.gro -s yyy.tpr -o xx_pbc.gro -pbc nojump
trjconv -f xx.gro -s yyy.tpr -o xx_pbc.gro -pbc mol
or
trjconv -f xx.gro -s yyy.tpr -o xx_pbc.gro -pbc cluster
and select your protein+ligand from index file (use index file in command -n index.ndx )
visualize again and see.
- Badges
- Science topic
- Similar topics
- Biological Science
- Kinesiology
- Running