[gmx-users] Exdending

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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