Dear Gromacs Users I wanted to study the interaction between a small molecule and protein. I prepared the system by inserting small molecule -nmol and protein by genbox and then I solvated it with water. when I tried to do PR dynamics it started giving many LINC WARNINGS. I reduced the time of equilibration and then PR run was completed without any warning. When I used production run it started giving LINC warning.Even after setting GMX_MAXCONSTRWARN to -1 I am getting LINC warning and programme termination with fatal error. Instead of simple docking I want to do MD with GROMACS to see interaction between the two molecule. Please suggest me, how can I do this. Thanking you.
Shahid Nayeem
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