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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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