Hi Vytas,
I tried it and it does helps. Now the question is to what extent one scales the dummy masses or the angles or the dihedrals? I used a pretty large number(100) for masses, angles and dihedrals and everything seems to be fine with it. But then it would be unrealistic for a dummy atom to have a mass of 100.008.
And for the simulations I had encountered LINCS error, I also used https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496/3?u=s.pallav all-bonds in constraints and the simulation seems to be fine.
Regards,
Pallav