GROMACS version:
GROMACS modification: Yes/No
Hello, I am new to GROMACS. I have modelled a nucleosome structure. When I try to minimize, one end of the DNA strand(about 2 bp) are completely displaced and the structure is distorted.
Any suggestions on how I can surpass this problem?
Thanks in advance!
Large changes during energy minimisation indicate that there are problems with the initial structure, such as atoms overlapping or very unfavourable bond lengths/angles. Such problems can often be circumvented by applying restraints during the EM stage.
You should also make sure that what you think are a large displacement is not just a problem of visualising atoms crossing the periodic boundaries of the simulation box.
I could solve the problem. thank you!