How to use pbc wrap command in vmd to re-center a multimeric protein?

Hi all, I have done this countless time and I've "googled" this a lot. Unfortunately I have a simulation that simply won't behave. 

I am trying to visualise (and analyse) a trajectory in VMD after removing the periodic boundary conditions. It is a helical dimer (important, as I need to consider bonds over the box and also two separate peptides separating over the box), in a box of water. During the first frame the dimer is whole in the box.

I have tried many combinations of trjconv with little success. The most logical, as per the Gromacs web site was: 

trjconv -f human_npt_0_40ns.trr -s human_npt_0_40ns.tpr -pbc whole -e 2-o firstframe.gro

I checked the first frame - it is present as t=0.000. The protein (dimer) is whole in the box.

trjconv -f human_npt_0_40ns.trr -s firstframe.gro -pbc nojump -o nojump.gro

In VMD this displays lots of very long bonds i.e., passing through the unit cell to the other side - no good. I tried this option again with -center on the protein. Still no good. I tried to centre the protein for the trajectory after -mol nojump. Still wouldn't work. I am technically not sure what has happened here. On a similar simulation of a dimer, from the above two commands I was getting a beautiful trajectory in VMD. This would suggest that my reference file to the -pbc whole is incorrect, it is not. 

Short of listing every possible combination of -pbc I will leave this here and hope that someone has some insight into removing tricky periodicity from GROMACS trajectories. 

Thanks

I used "draw delete all" command to delete the pbc box in VMD, but it's just removed from the current frame. How can I remove it from all frames?

Dear all,

I have been trying to "wrap" my protein in the trajectory using the following command, using VMD:

I am not sure if it works, because even though I can see how it process the frames,   all atoms appear in white and proteins does not move at all. 

Also, when I try to save my trajectory by using:

anímate write dcd new.dcd sel $sel         my trajectory is not saved

Do you have any recommendation?  I would really appreciate them.

Thanks in advance.

Hello every body

I want to calculate the center of mas for a protein. I want to know which amino acid the center of mass hold on.

pleas give me a full help.

thanks

I tried to run a 500ns MD simulation of a protein in Gromacs. Due to power failure, my pc turned of after around 450+ ns. Now I want to restart the simulation from that point. I used the following command-"gmx mdrun -v -deffnm md_0_1 -cpi md_0_1.cpt -append", but found that I dont have any cpt file. Now how should I do this? Is there any other way? If not, then how to generate the cpt file of my simulation?

I was trying to apply restraints on my molecules, however, they were still moving after I put 100000kJ/mol/nm^2 on them. I am sure my topology is correct, so I think maybe its the correlation of atom name that is causing all the troubles. I constructed my pores.itp by entering all the molecule fragments I wanted to keep still, while looking at the in.g96 displayed on vmd. Still, I am not sure where the problem is. Do anyone have any suggestions?

After simulations, how to write the pdb file of a particular frame in VMD (containing protein +ligand)?

I did simulation using NAMD and wrapall = on option. While saving the coordinates in pdb format from the trajectory format, I want to unwrap the molecule.

I have a protein embedded in lipid bilayer. At some point, my protein moved towards the edge of simulation box. I applied PBC wrapping so the box is centered around protein. However, the trajectory now constantly adjusts itself to the protein which makes it hard to record a simulation movie. I would like to make it so the trajectory stays in place while also centering the protein.

Is it possible to keep the trajectory in place while viewing on camera? If not, is it possible to make the camera follow the trajectory?