GROMACS version:
GROMACS modification: Yes/No
Here post your question : Please clarify my doubt on How to set -dt and -b options in gmx trjconv… And what effect does it have on number of frames…
Thank you
I have checked the provided link, but still I didn’t understand on how to set these values… On what basis… Please help me with that…
You set whatever values you need; if you want to skip the first X ps of the trajectory, use -b X, and if you want to skip some frames, you can use -dt but -skip is easier to use.
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But sir, Why is there a need of deleting frames… Doesn’t it affects our results??
There are many reasons to shorten a trajectory or divide it into segments to do various analyses. There is no requirement to do this.
okk sir… Thank you soo much…
Can you please help me on how to build Markov state models using simulation data…
That’s not something GROMACS does natively. You’ll have to look into other software to build an MSM.
Ya… Thank you sir… Can you please help me on how to make Force-extension curve using simulation data…
It would be better to start a new discussion thread if you’re asking unrelated questions.
okk sure…