unanswered Martini3 protein simulation keeps crashing

  • anjukris
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2 months 1 week ago - 2 months 1 week ago #9514 by anjukris

I have been trying to use Martini3 + the latest Go-like model to simulate the approach of two large protein subunits in water. I have followed the tutorial from the workshop in 2021. I was able to get around 5 microseconds of sampling, but when I tried to extend the simulation using the Gromacs checkpoint file, the simulation starts throwing up LINCS and pbc warnings at the 5.7 microsecond mark.

Here's a brief overview of my methodology:
Since I have two proteins in my system, I generated Go parameters for each of them independently as described in the tutorial (I didn't want Go-like bonds between them). To this end, I defined two different GO_VIRT variables in my topology file -
#define GO_VIRT
#define GO_VIRT2
one for each protein.

I changed tau-p to 8 from 12 to see if that would make a difference but no luck.

On the other hand, the tutorial simulation worked fine. I have tried it on another small protein which worked well too.
Help would be greatly appreciated!
Last edit: 2 months 1 week ago by anjukris.

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