[gmx-users] Protein-surface interaction during flow

[Kamps, M.]

Dear Micholas,

Thanks for your reply and suggestions!

Your idea at point 2, how can I do this? The forces and velocities are
stored in the .edr files, while the final velocities and positions are
also stored in the output .gro file right? This means I should run a
simulation just long enough that the proteins reach a desired point,
after which I can use the final .gro  or the .edr files?
I then need to continue (extend) my simulation, while creating a new
.tpr file via the new .mdp file, effectively using this command:

gmx grompp -f new.mdp -c old.tpr -o new.tpr -t old.cpt
mdrun -s new.tpr
(http://www.gromacs.org/Documentation/How-tos/Extending_Simulations)

Will this continue my simulation with the 'previous' velocities? Since
none of these files will input any .edr or .gro files?

Mark