[gmx-users] Exdending

Justin Lemkul jalemkul at vt.edu
Thu May 2 17:04:27 CEST 2013

On 5/2/13 11:01 AM, Dubi wrote:
> Dear Gromacs Community,
> I m in the situation where I have a trajectory that started in a geometric
> position "A" and ended in position "B". If I hit a new mdrun with the
> "-append" extension, than the trr output is the old trajectory together with
> the new one which starts at position "B". Unfortunately I want the new trr
> output to be the old trajectory together with the new one which should start
> again at position "A".  The new trajectory should differ from the old one,
> since I have random seed on.
> My question is, how do I get gromacs to do that? Is it enough if I just
> don't pass a Checkpoint file, or should I construct a checkpointfile from
> the first frame? To get a checkpointfile from the first frame I guess I have
> to start a trajectory with 1 timestep - or is there a smarter way?

You can't build a new checkpoint file like that.  It sounds to me like you just 
need to run a new simulation.  Setting gen_seed = -1 generates a random seed for 
velocities, but those velocities are then stored in the .tpr file; they are not 
re-generated randomly when mdrun begins.

I think what you need to do is just run a new simulation.  If you want to append 
it to your existing .trr file (for whatever reason), that's what trjcat is for.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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