I found your comments in gmx-user communications. I’m using gmx 453,
with DNA system. Pdb2gmx is ok, but gmx treated each string as protein.
I used command
pdb2gmx -f new.pdb -o wt.gro -p wt.top -water tip4p
then choose charmm27 ff,
everything looks good. However I found during my md runs, DNA separated.
System goes to weird. Do I need to remove TER between the paired stands?
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