[gmx-users] Time step mismatch.

[Christian Blau]

Hello Maryam,


trjconv might help here. There are two ways I can interpret time step in your email.

  1. the integration time step dt - if you changed this one I would not recommend that you concatenate the trajectories 
(though also possible), but treat this as independent simulation setup, because this will mean a different approximation 
to the underlying physics.

      there is an option in trjconv  -timestep <time> (0) Change time step between input frames (ps)

  2. the output frequency

      There, the trjconv options -skip   <int> (1) Only write every nr-th frame
                                                    -dt <time> (0) Only write frame when t MOD dt = first time (ps)

      should help to generate trajectories that have matching spacing time.


Best,

Christian


On 11/6/19 11:15 AM, Maryam wrote:
> Dear gmx users,
>
> I have two xtc files generated from my simulation with two different
> time steps. I had to change the time step/mdp options because of disc
> size. After the simulation, I tried to use trjcat to combine the two xtc
> files so I can perform analsis on the trajectory. But I get this warning  :
>
> Timesteps at t=1.4028e+07 don't match (1200, 1500), How do I fix this?
> is it possible to rewrite the time step after the simulation?Thanks in
> advance.
>
> Best regards,
>
> Maryam
>
>
>
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