[gmx-users] unusual trajectory

Alex nedomacho at gmail.com
Tue Jul 24 22:43:56 CEST 2018

I said other things as well, i.e. you could have issues with setup. 
Noone knows if your trajectory is "appropriate" and noone knows if your 
setup is correct.

Could you upload your trajectory somewhere and tell everyone what you 
think is wrong? Also, I recall both Justin and myself telling you to use 
appropriate box size in the CNT's axial direction. Did you do that?
Also, what is your forcefield? Why are you using short (0.9 nm) cutoffs? 
Why are you thermally coupling all your subsystems separately? Why are 
you turning all CNT bonds into constraints? All these questions need to 
be answered before one starts taking trajectories seriously.


On 7/24/2018 5:49 AM, Atila Petrosian wrote:
> Dear Alex and gromacs users,
> I used trjconv -pbc whole. But my problem was not solved.
> You said "What I am trying to say is that per se nothing wrong seems
> to be happening". As I uderstood, in analyses such as gmx rms and
> gmx distanc and gmx traj (which I need them) this trajectory is not
> appropriate and should be corrected and modified.
> Which option of trjconv solve my pbc problem?
> Best regards,
> Atila

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