Re: [AMBER] [cpptraj] Changing frames in a trajectory file

From: Juan Eiros Zamora <>
Date: Tue, 16 Jun 2015 20:44:19 +0100


I was thinking that when I analyze the trajectories, whenever I do a
plot that has the simulation time in ns and not the frame number, I
don't have a constant time step to convert from frame to time.

If not I can always apply a different conversion for those 50 ns, but I
thought it might be easier to modify the frame number in the trajectory
than doing that.

So it might be not that critical, but I was wondering if there was a
possibility to do it (truth is I've made the mistake for four of my
runs, so I have four different files to change)

On 16/06/15 20:27, Hai Nguyen wrote:
> hi
> I don't have an answer but just want to ask why is it so critical to get
> the same #frame?
> Hai
> On Tue, Jun 16, 2015 at 3:19 PM, Juan Eiros Zamora <
>> wrote:
>> Dear Amber users,
>> By mistake I modified the write frequency of a production run and ended
>> up with a 50 ns NetCDF trajectory file that has a bigger number of
>> frames (4000) than what I usually use (2500).
>> My problem now is that I want to reduce the number of frames of that
>> file to match the other trajectories of the same run, but as you can see
>> the ratio is not an integer so I've had no luck using cpptraj, as it
>> does not allow me to chose an offset of 1.6 for the trajin command.
>> I'm wondering if there could be a way to "interpolate" structures in the
>> trajectory so I could get a constant timestep.
>> Does anyone have a suggestion or idea on how should I proceed with this
>> issue?
>> Thanks in advance,
>> Juan
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Received on Tue Jun 16 2015 - 13:00:02 PDT
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