As you may have seen in the GROMACS 4.0 manual, "Walls can only be used with pbc=xy" so its more of a floor/ceiling. You still may want a solution beyond the feature mentioned in chapter 7. Particle based realizations for walls may be a bit more work but very doable. See the following paper.
Chenyue Xing and Roland Faller J. Phys. Chem. B, 112 (23), 7086-7094, 2008. -Matt ------------------------------ Message: 3 Date: Sat, 11 Oct 2008 10:41:39 -0400 From: "Justin A. Lemkul" <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Simulation of a protein confined in a box To: Discussion list for GROMACS users <[email protected]> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Lee Soin wrote: > This seems to me a very complicated realization. Why doesn't > GROMACS provide an easy way for wall simulation? > How about reading manual section 7.3.20 "Walls" in the Gromacs-4.0 manual? I think that would be what you're after. -Justin > 2008/10/11 Omer Markovitch <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> > > Oh, I didn't read carefully. > My suggestion would be, perhaps, to physically put atoms on the > sides of the box (possibly, fill each side completely), and to place > on them very high repulsion. > You might want to freeze them up, and exclude their self > interactions from the energy calculation. > > Good guess Suman. Omer. > > > Koby Levy research group, > Weizmann Institute of Science. > http://www.weizmann.ac.il/sb/faculty_pages/Levy/ > > > On Sat, Oct 11, 2008 at 09:26, Suman Chakrabarty > <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote: > > Possibly what he is interested in is a system WITHOUT PBC? I > don't think > with PBC the system is really "confined", since there is no true > wall to > reflect the colliding molecules. Thus to study the effect of real > confinement, it is necessary to remove PBC and impose reflective > boundary conditions. I am only guessing! :) > > > --Suman. > > > > _______________________________________________ > gmx-users mailing list [email protected] > <mailto:[email protected]> > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before > posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > -- > Sun Li > Department of Physics > Nanjing University, China > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
