Problems concatenating trajectory

[alessandronascimento]

Hi Make-it-rain guys,

First of all, thanks for this awesome tool! I loved the idea!

I'm running a simulation using AMBER input, which I generated before using leap.

Everything was ok in the colab up to the point where I am trying to concatenate the trajectories. In this step, I have the following error message:

---

IndexError Traceback (most recent call last)

in () 20 21 trajlist = pt.load(flist, pdb, stride=stride_traj) ---> 22 traj_image = trajlist.iterframe(autoimage=True, rmsfit=0) 23 traj_write = pt.write_traj(traj_end, traj_image, overwrite=True) 24 traj_load = pt.load(traj_end, pdb)

1 frames

/usr/local/lib/python3.7/site-packages/pytraj/trajectory/trajectory.py in getitem(self, index) 303 """ 304 if self.n_frames == 0: --> 305 raise IndexError("Your Trajectory is empty, how can I index it?") 306 307 if is_int(index):

IndexError: Your Trajectory is empty, how can I index it?

---

It does not seem to be system dependent, since I tries two different systems already with the same issue. Any ideas of what might be going on here?

Thanks.

[pablo-arantes]

Hi @alessandronascimento,

Thank you so much for your feedback. We are very glad to see people using Making it Rain. Regarding your issue, I tried here and everything worked fine for me. I was able to concatenate the trajectory on Amber_inputs notebook. I have one point to make, if your notebook disconnected, you should run again the cells with the same parameters (from the beginning). The code will recognize your files, and it will not run again the production step. Please, remember to use the same parameters, as Stride_time, Number_of_stried and so on. This is necessary because some variables are declared in the previous cells in the notebook.

Please, let me know if it is working.

Thank you.

Best,

Pablo

[alessandronascimento]

Obrigado, Pablo!!!

I think you found the issue! Actually, my notebook was disconnected a few times during the MD and I just reconnected and ran again a few of the code cells (not all of them). I'm repeating now as you suggested and will let you know about how it goes.

Maybe a suggestion: is it possible to modify the minimization/equilibration code to check if the equilibrated trajectory already exists and skip the minimization/equilibration just like the MD cell does? I think that this little change would be of benefit in cases like mine, where the notebook gets disconnected!

All the best and thanks again,

PS: I think you can close the issue I opened!

Alessandro

Em qua., 11 de mai. de 2022 às 04:59, Pablo Ricardo Arantes < @.***> escreveu:

Hi @alessandronascimento https://github.com/alessandronascimento,

Thank you so much for your feedback. We are very glad to see people using Making it Rain. Regarding your issue, I tried here and everything worked fine for me. I was able to concatenate the trajectory on Amber_inputs notebook. I have one point to make, if your notebook disconnected, you should run again the cells with the same parameters (from the beginning). The code will recognize your files, and it will not run again the production step. Please, remember to use the same parameters, as Stride_time, Number_of_stried and so on. This is necessary because some variables are declared in the previous cells in the notebook.

Please, let me know if it is working.

Thank you.

Best,

Pablo

— Reply to this email directly, view it on GitHub https://github.com/pablo-arantes/making-it-rain/issues/18#issuecomment-1123316242, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADSXQFKI737RRT43SD25CTDVJNSH3ANCNFSM5VSGY44A . You are receiving this because you were mentioned.Message ID: @.***>

[pablo-arantes]

Hi @alessandronascimento,

De nada... ;-)

Thank you so much for your feedback and your suggestion. For sure, we will try to implement that.

All the best,

Pablo