Re: diffusion of protein into water box

From: Ramin Ekhteiari (ramin_ekh_at_yahoo.com)
Date: Mon Nov 25 2013 - 02:30:39 CST

My problem is solved when I use this commands **pbc wrap -centersel "protein" -center com -compound residue -all** Ramin On Sunday, November 24, 2013 4:26 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote: On Sun, Nov 24, 2013 at 3:21 PM, Ramin Ekhteiari <ramin_ekh_at_yahoo.com> wrote: > Is it reasonable? ( diffusion of protein ). why should it not be reasonable? have you check the (many!) discussions on that same subject in the mailing list archives? might be enlightening... ;-) > But when protein cross the > boundary of the box, the periodic images will > interact with themselves affecting the outcome of the simulation. i don't understand what this is supposed to mean. axel. > > 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. > > > -- Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.

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