[AMBER] During MD simulation protein drifts out of periodic cell

From: Michael Shokhen <michael.shokhen.biu.ac.il>
Date: Sun, 7 Jun 2015 13:35:23 +0300

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

 Thank you,


Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
email: michael.shokhen.gmail.com
email: shokhen.mail.biu.ac.il
AMBER mailing list
Received on Sun Jun 07 2015 - 04:00:03 PDT
Custom Search