GROMACS modification: No
I have encountered some problems after using Gromacs 2019.6 to simulate a 36bp long double-stranded DNA in water and ionic solutions(X Y Z of box size: 14.66438nm x 6.70097nm x 6.82766nm) and I can’t solve them. The specific problems are as follows:
Fisrtly, I have carried out a 500ns simulation for dsDNA in solution without setting the md.mdp of removing center of mass translation and rotation around the center of mass(comm-mode = Angular ; comm-grps = DNA). Then I use gmx_trjconv to deal the md trajectory(use first gmx trjconv -f md.xtc -s md.tpr -o md_mol.xtc -pbc mol -center, then gmx trjconv -f md.xtc -s md.tpr -o md_nojump.xtc -pbc nojump -center, and try -pbc atom , -pbc whole). After visualize the PBC dealed md trajectory , the single chain of dsDNA is separated and the complete double-stranded DNA molecules can not appear. I want to show the complete double-stranded DNA molecules conformation in my article. Secondly, I I have carried out a 500ns simulation for dsDNA in solution with setting the md.mdp of removing center of mass translation and rotation around the center of mass(comm-mode = Angular ; comm-grps = DNA). The same problems occurred when I deal the md trajectory file in the same way, except that it didn't appear in the first 100ns of the simulation, but it appeared later. Note:I try dealing the PBC of md trajectory with VMD. However the problem remains unsolved. How I can solve it. Thank those who can help in advance.