[gmx-users] Fwd: Enquire about double strand DNA in gmx 4.5.3 charmm27 ff.Thank you.

David van der Spoel spoel at xray.bmc.uu.se
Sat Feb 26 10:27:59 CET 2011

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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