VMD data analysis automatization (part1): Load, wrap, align, and calculate RMSD of trajectory

[@정민준-q6l]

Hi mohamed thank for video,
what is different pbc wrap and pbc unwrap?

[@amaransi4900]

hi Mohamed, Could you please provide us how to read large dcd file

[@Xiaoxinxin_in_south_Alps]

Hello. Thanks for sharing. I managed to do it but I dont know where is the putput file rmsd.dat and rmsf.dat. Could you help?

[@mrYazeed1122]

Thanks for your videos. For uploading the script: try uploading it on a google doc and sharing the link on the description

[@Mohamedshehata]

Done!

[@हरिःओमतत्सत्]

​@@Mohamedshehata where is the link to script file? Thanks in advance.

[@omidghobadiha4599]

very good thanks

[@Mohamedshehata]

you are welcome!

[@shreyabhattacharya3455]

Can you share the script?

[@royajafari9028]

the pbc command doesn't work in this way. It says "invalid command name pbc"

[@ananyayadav4337]

how we calculate rmsf for specific resudues of my protein

[@Mohamedshehata]

change your selection as you wish

[@grigore-mihaitastan2481]

Hello sir! Nice content. I would need some help in trying to compute RMSD between 2 proteins. Can you please pm?