Dear Justin, Thank you very much from your time.
Best Regards Sara ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: mohammad agha <mra...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Monday, October 15, 2012 9:54 PM Subject: Re: [gmx-users] about equilibrium I didn't see anything inherently wrong with your previous observations, so I suspect your new approach is probably fine. There are several ways to do just about anything; you just need to find one that works to your satisfaction and represents a reasonable model of whatever you're trying to simulate. -Justin On 10/15/12 12:37 PM, mohammad agha wrote: > Dear Justin, > > The previous problems was as is following: > >> 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 > >> 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. > > Please define what you mean here. You start with a 6-nm > cubic box. How small does it get? Are the box vectors trending > downward, or do they converge? What is the change in density, and is it > acceptable? > >> According what you said, when the box become smaller in equilibrium, there >> is not mistake and it is natural? >> > > That > depends on the magnitude of the change. Compression indicates that the > pressure (and thus density of the system) was not at the desired value > and the system is contracting. The manner in which the contraction > occurs (magnitude, speed) is the deciding factor as to whether or not > there is a problem. > > also, > > >> Dear Mark, >> >> >>> May I know your idea about cause of my doubt, Please? > > As I said yesterday: > >> At least one of your volume, contents or model physics are not >> consistent with the others, but only you can say which. > > Since only you know anything about your volume, contents and model > physics, or that of the work you think you should be replicating, we > can't help at the moment. See previous comment about relevant > information :-) > > Mark > >> >> Best Regards >> Sara >> >> >> >> ----- Original Message ----- >> From: Mark Abraham <mark.abra...@anu.edu.au> >> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> Cc: >> Sent: Friday, October 5, 2012 9:34 AM >> Subject: Re: [gmx-users] equilibrium for box of simulation >> >> On 5/10/2012 3:55 PM, mohammad agha wrote: >>> Dear Justin, >>> >>> Thank you very much. >>> So, decreasing of box dimensions is not bad, if all thing process natural, >>> yes? >>> > The cause of my doubt was because of in the most of articles was said > for example " we select box with dimensions 10nm that after equilibrium > was converted to 11nm" and I didn't see the report of decreasing of box > dimensions! May I know your idea about it, Please? >> Following a > published method closely and observing an opposite result is a cause for > concern. You have to judge "closely," however. You should have said > earlier this was one of your reasons for doubt, rather than leave us to > guess. The quality of the help you might receive is often in direct > proportion to the quantity of relevant information you give in asking > for it. >> >> Mark > > > ----- 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: Monday, October 15, 2012 7:50 PM > Subject: Re: [gmx-users] about equilibrium > > > > On 10/15/12 12:11 PM, mohammad agha wrote: >> >> >> Dear Justin, >> >> Thank you very much from your response. This question was because of my >> previous problems about equilibration the box that I sent it with subject >> "equilibrium for box of simulation". When I equilibrate solvent and >> additives separated and then add to surfactant and after that equilibrate >> totally, there are not previous problems and I wanted to know that this >> method is correct? >> > > Please provide a link to the previous thread. I read hundreds of posts per > week; I don't recall this one. A sequence of commands would also be helpful > here, as I cannot clearly envision what you are describing. > > -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. 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