Re: diffusion of protein into water box

From: Ramin Ekhteiari (ramin_ekh_at_yahoo.com)
Date: Sun Nov 24 2013 - 08:21:04 CST

Is it reasonable? ( diffusion of protein ). But when protein cross the boundary of the box, the periodic images will interact with themselves affecting the outcome of the simulation. Ramin. On Sunday, November 24, 2013 4:14 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote: On Sun, Nov 24, 2013 at 3:06 PM, Ramin Ekhteiari <ramin_ekh_at_yahoo.com> wrote: > Hi, > > I did a MD for a protein at a water box via NAMD, but during simulation the > protein diffuse along the box and cross the boundary. > > Would be grateful for any help. help to do what? axel. > > Cheers, > Ramin -- Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.

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