GROMACS version: 2024.2
GROMACS modification: No
Hello,
I am facing a problem with protein-ligand simulation box created using the standard tutorial. The “.gro” file created during the last step looks like weird when loaded in VMD.
Seems like, the simulation box is broken at few areas, and complex is also not compact.
I have performed quite a many simulation before, and never faced any issues like a broken simulation box.
Although after I centered the XTC file, visualized them again in VMD, it looked fine; and got RMSD values in expected range, but the GRO file scares me.
Is it common? Or did make any mistakes during the setup?
I remember getting some warning in NPT and NVT equillibration steps saying. “WARNING 2 [file topol.top, line 53735]:
** Too few parameters on line (source file**
** /home/Desktop/GROMACS/gromacs-2024.2/src/gromacs/gmxpreprocess/toppush.cpp,**
** line 1899)**”.
But was not sure what might have gone wrong, so had overwritten it with “maxwarn 2”.
Any help would be highly appreciated.
Thank you!