Visualization, run single LAMBDA folder, and extension of simulations

[Oulfin]

Hi,

When I try to visualize the trajectory with pymol, I see that the ligand and protein are in different parts of the water box (due to the periodic boundary conditions) and this is making hard to analyze the data visually to understand if residues nearby the ligand should have different protonation like Histidine etc... Is there a way to fix this or that is why there is the VMD script available?

My simulation stopped at the last LAMBDA_1.00 without finishing, is is possible to run only that folder and not the whole thing again? I use --run_type=run, so I am not sure what is really doing.

Is it possible to extend the simulation run, for instance from 4 ns to 8ns? Is there a way to do so in the command line?

Thanks!

Best,

[adw62]

Hiya,

I think the VMD script provided is just for visualizing the hybrid molecule initially not for the trajectory. Generally though I would use an external program like VMD or GROMACS to unwrap simulations. I think in VMD its something like pbc unwrap -all

You can rerun a sub set of windows with the cli option --windows_mask=7,8 this take a python range of windows to run, so there you'd run window 7.

There is no option for extending simulations. If you want to add more sampling to improve the accuracy and precision of the result we find the better way to do this is to add replicas rather than for running longer simulation. If there was a use case where you regularly needed to extend simulations I could definitely add this as a feature though.

Cheers, Alex

[Oulfin]

Hi,

Thanks for the information.

I also managed with cpptraj like this: parm .prmtop trajin .dcd fiximagedbonds autoimage trajout reimage.dcd run

I agree with you that with more replicas you can improve the sampling. I do not think I will use the extension of simulations.

Best,