Dear ResearchGate community,
I have recently conducted two separate 100 ns molecular dynamics simulations using GROMACS, each involving a small molecule. My analysis of hydrogen bonding patterns has revealed an unexpected observation: zero hydrogen bonding and an unusually large number of pairs within 0.35 nm. For instance, at a specific time point (e.g., time = 1.90108e-33 ns), the number of hydrogen bonds reported is >1110000000. I would like to know about such variations and how should I fix it, and if anyone has insights into the potential implications of this observation. I appreciate any feedback or experiences you can share on this matter.
; Include forcefield parameters
#include "./charmm36-mar2019.ff/forcefield.itp"
; Include ligand parameters
#include "crx.prm"
Thank you
Hi Alireza! At the specific time point (time = 1.90108e-33 ns) you actually have zero hydrogen bonds according to the file which you uploaded here. You have a big number of hydrogen bonds after 97 ns. However, I couldn't find which groups you used for your calculation? I would suggest you to try not to use "-tu ns" in your calculation. I think what you observe can be related also to time units which you specified. Try to use the default, ps. Then select the right groups in you index file and compute again. I haven't had such an issue before liie the one I see in your xvg-file, but I suspect that Gromacs might have some output problems with digits when your time is in ns.
The data contains some anomalies, such as values that are too high or too low and zeros that appear repeatedly in the file. These values do not represent the number of hydrogen bonds. Moreover, the time legend is wrong. These problems may suggest that the data processing was faulty, perhaps due to selecting incorrect groups.
Well, if you look at the column for the time which is the first column of all, you will see zeros there too! That is why I suspect that what you computed has issues with time-units which you wrote after "-tu" flag. The legend is correct but the values are zero until around 97.92 ns.
Alireza Mohebbi Can you please check the you have chosen the groups while analysis? Hope that will give the correct results.
I agree Inna Ermilova
Thank you all for your time and suggestions. Unfortunately non of the above mentioned recommendations resolved the issue. I have done some other modifications, but they also did not resolved the outcome.
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