Well, the different starting coordinates for the replicate simulations come from a pre-existing trajectory calculation (of which snapshots are taken at regular intervals to provide the different starting points), hence the possible relevance of previous restarting data.
Thank you both for the replies.
I think there's a bit of confusion in terms of charmm's syntax. I think what you're asking is how to start dynamics anew from points along your original trajectory, no?
You've referred to that as "re-starting" them, but strictly speaking to restart dynamics using the DYNA REST command is to
continue them, as Lennart and Rick have been saying. In other words, in charmm REST = continue dynamics by picking up where you left off.
If I've understood things correctly, you want to DYNA STARt from the coordinates taken from your original trajectory but with new (randomly assigned) velocities (you could also perturb the old ones, I suppose). You can use the IASORS .eq. 0 to assign new velocities and you can use IASVEL to select how to assign them. I imagine you'd want to use the Gaussian (IASVEL .gt. 0). You'll want to take care that the new velocities are appropriate for the temperature of the simulation (see TSTRUC in dynamc.doc, e.g.).
