AMBER Archive (2002)

Subject: DNA shifts during MD; C.O.M. removing and ptraj doesn't help...

From: Filip Ryjacek (filip.ryjacek_at_jh-inst.cas.cz)
Date: Thu Apr 18 2002 - 10:17:12 CDT

Hi all,
need help with following problem:

I need to analyze first+second solvation shell around DNA in water, but
during MD (DNA+water) the DNA shifts and rotates in box. IWRAP and NSTCOMM
options are set, C.O.M. motion is periodically removed. Ptraj doesn't help,
resulting trajectory is the same as input trajectory.
I hope problem is in ptraj, but I cannot find where...

Thanks in advance for any hints,
        Filip