Dear Justin, "my materials are not placed in the smaller box" means if I select box with dimensions 5.99 nm, space is low and insufficient for my molecules! but after equilibrate the box become small. According what you said, when the box become smaller in equilibrium, there is not mistake and it is natural?
Best Regards Sara ----- Forwarded Message ----- From: Justin Lemkul <jalem...@vt.edu> To: mohammad agha <mra...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Thursday, October 4, 2012 5:52 PM Subject: Re: [gmx-users] equilibrium for box of simulation On 10/4/12 10:06 AM, mohammad agha wrote: > Dear GROMACS Users, > > I asked this question before but I don't understand it! > > > I placed several materials in my box of simulation for example box with > 6nm*6nm*6nm and my materials are not placed in the smaller box but when I > equilibrate my system, the box became smaller and temperature and pressure > also equilibrate. my question is: is my system and equilibrate mistake, > because of reach to smaller box? Is there equilibriums with reach to smaller > box? > > What do you mean by "my materials are not placed in the smaller box"? If a box compresses, it is because the initial configuration was incompatible with the desired equilibration conditions and it contracted produce the desired quantity (likely pressure). -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist 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 gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
