[gmx-users] Reading starting velocities

Ignacio Fernández Galván jellby at yahoo.com
Fri Mar 9 13:29:31 CET 2012

Hi all,

I was wondering if it's possible to start a simulation by reading the starting configuration from a file and the initial velocities from somewhere else. The goal is being able to "continue" a simulation of a mostly equilibrated system, but where I change slightly the coordinates of some atoms (in particular, of some frozen atoms).

The closer I could get to that was modifying the final .gro file of the first simulation, which includes coordinates and velocities. But the precision of the .gro file is relatively low. I tried using both a .gro (without velocities) and .cpt files for starting the new simulation, but initial velocities are then assigned as 0.000. I also tried trjconv to convert the .cpt to .gro with higher precision (-ndec), but only coordinates are written in this case (although I explicitly added -vel). I guess I could manually add the velocities after getting them with gmxdump, but is there some other more straightforward way?


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