Dear Amber List members,
I have observed that already after 5 ns MD simulation
a protein molecule is considerably shifted
toward one of the side of cubic periodic box.
Obviously that with such a trend after hundreds ns simulations the protein
will drift out of the periodic box.
In my simulation I used iwrap=1 that keeps imaging of water molecules
in frames of periodic box. But how to avoid diffusional drifting of protein
out of periodic box? I guess there should be a command that keeps the
protein center of mass on its initial position during MD simulation.
I am a new amber user and I would appreciate if somebody advise
me what commands should be added to the md.in script to prevent
protein drifting and keep the protein center of mass on its initial
position.
Thank you,
Michael
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: michael.shokhen.gmail.com
email: shokhen.mail.biu.ac.il
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Received on Sun Jun 07 2015 - 04:00:03 PDT
