Is that possible to update the hbond calculation without generating a new trajectory file?

User discussions
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GROMACS version: 2018.8
Hello,
I have finished my simulations. I used a low frequency to output the .xtc trajectory file, otherwise the size of the trajectory files would be too large for me to store on the hard disk since the number of my simulations is a little large. But I found that in this case, when I use the hbond to get the hbond numbers, the output frequency is also too low since it is the same as the trajectory file.
I want to increase the output frequency of the hbond information. I am wondering whether it is possible to do the hbond analysis without generating a new trajectory file? Or I must rerun the simulation and generate a new trajectory file with increased output frequency?
Any help would be much appreciated!

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Hi,

If the analysis requires more frames you will have to rerun with more frequent output.

If you know which groups you will perform the analysis on (and it’s not the entire system), you could save space by writing the .xtc information for them only at a high frequency. Use the compressed-x-grps option in your .mdp file. If needed, you can also get the full system trajectory at a lower frequency by setting nstxout to a lower frequency. This writes a .trr file.

Regards,
Petter

3

Hello,
Thank you very much for the reply!
Sorry, I do not understand the last part of your reply.

If needed, you can also get the full system trajectory at a lower frequency by setting nstxout to a lower frequency. This writes a .trr file.

Do you mean for the whole system I use a low frequency to output .trr trajectory? and for the groups that will do hbond analysis, I use a higher frequency to output .xtc trajectory?
Thanks very much in advance!

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Yes, precisely – if you also want the full system trajectories but don’t need that at the same output frequency. But if you don’t care about that, setting nstxout-compressed is sufficient. Example:

nstxout = 1000000 ; 
nstxout-compressed = 5000 ; frequent output of protein only for analysis
compressed-x-grps = Protein ;
5

Hello,
Thank you very much for the explanation!
The .trr file would be too large for me. I think I will not use the information of velocity, so I guess I only need .xtc files at this moment.
Even the output .xtc file at a low frequency is too much for me since I have many paralleled simulations.