[gmx-users] Position Restraint or remove COM from DNA

Hovakim Grabski hovakim_grabski at yahoo.com
Sun Nov 30 21:34:07 CET 2014

Dear Gromacs Users,I'm trying to run a simulation between a Dickerson dodecamer(12 basepair DNA) and 6 molecules of Methylene Blue.My  1 question is:
If I try to  remove COM from DNA, it gives an error, so I have to set comm_grps  = System, but 1) doesn't that affect the Methylene Blue molecules?2) is there any way to  remove COM from DNA without getting an error?
2. Or should I just use position restraint on DNA's 5' and 3' ends on one strand?
Thanks in advance,Hovakim

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