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AMBER Archive (2009)Subject: Re: [AMBER] RE: question
From: rrd (rrd_at_seznam.cz)
Hi Ross,
thank you very much for helping us.
How wrote Marek, we have problem with freeze atoms. I use ibelly for it and after simulation, atoms aren't on same place as on the beginning of simulation. For example, I use this input file for heating my system.
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According to ibelly and bellymask, only residues who can move are LGM and WAT (LGM with restraint), but result is different (see pictures - links below - which show states freeze atoms before simulation and after). On pictures, points are C atoms (without charge) and on top are H-O-H atoms (with qH=0.053, qC=-0.106). For simulation I use sander.MPI.
Again, really thank you for any advice.
Pictures:
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