Which parts should be used for MD analysis, whole trajectory or balanced trajectory?

User discussions
1

GROMACS version: 2021.1
GROMACS modification: No

Hello,
These days, I am learning the analysis of production MD result, but I am confused about that which parts should be used for MD analysis, whole trajectory or balanced trajectory?

For example, the following RMSD figure.
gpu3_QA

If I want to do the clustering analysis, and do DSSP analysis, which part of the trajectory should be used for these analysis? The whole trajectory (0-300ns) or the balanced trajectory (200ns-300ns)?

I noticed that most of the gmx comands, they have -b and -e options, so I did the analysis only using -b 200 -e 300 -tu ns, which is the balanced part.

Can you help give suggestions if what I did is OK?

Thanks.

2

Hi,
a standard MD protocols has an equilibration and data production. Once the system is equilibrated in the defined thermodynamic ensemble, one can start data collection and extract properties from the trajectory generared under data production

Note that you can use also -b X along that mean that the analysis will start from time X up to the end of the trajectory.

best regards
Alessandra

3

Hello @alevilla Thanks for your explanation. From your explanation Once the system is equilibrated in the defined thermodynamic ensemble, one can start data collection and extract properties from the trajectory generated under data production, what I did should be OK, because after 200-ns, it can be considered as data production stage by seeing the RMSD trajectory (above figure) an approximately flat with the time increasing to the end.

Thanks for letting me know that I can use -b X only.

One more question need be confirmed that for an equilibration and data production, can I check these two parts based on the RMSD plot as below?
equili_data production_check

Can you help confirm if what I understand about an equilibration and data production is correct? Also, NVT equilibration phase and NPT equilibration phase as in the tutorial (Lysozyme in Water) are not same as what you said an equilibration, right? What you said about an equilibration should be based on the finished production MD, such as based on the RMSD plot above, please help check if my understanding is correct?

Thanks,
Ming