Pressure scaling more than 1% in streed molecular dynamics

User discussions
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1

GROMACS version:2023
GROMACS modification: Yes/No
Hello, I’m running a smd simulation on peptide nanotube and drug system and did nvt and npt for 500 000 steps. Also I have used v-rescale and c-rescale algorithms, but I face the error “pressure scaling more than 1%”. Can anyone help me with this? Should I increase the number of steps of nvt and npt? Thanks in advanced.

2

is it cyclic peptide nanotube? yes, typically increase the nvt and npt, are you restraining the drug molecule to avoid drifting it apart?

3

thanks for your answer.
Yes it is cyclic peptide nanotube and I applied restraint to my nanotube and drug as well (the amount is 1000).
How many steps do you suggest me to consider? it’s 500 000 now…

4

can you show me the image of your simulation system, position of drug and CPN