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 -- gmx-users mailing listgmx-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
Re: [gmx-users] equilibrium for box of simulation
On 5/10/2012 4:12 PM, mohammad agha wrote: Dear Mark, Yes, you're right. Excuse me, for this and thank you for your reminder. 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 -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
Re: [gmx-users] equilibrium for box of simulation
On 5/10/2012 12:06 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? At least one of your volume, contents or model physics are not consistent with the others, but only you can say which. Mark -- gmx-users mailing listgmx-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
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 listgmx-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
Re: [gmx-users] equilibrium for box of simulation
On 10/4/12 10:38 AM, mohammad agha wrote: 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. -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 listgmx-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
Re: [gmx-users] equilibrium for box of simulation
On 10/4/12 12:25 PM, mohammad agha wrote: Dear Justin, Thank you very much from your help. Oh, yes, the vectors of box are downward in the first with much slope and then the slope became milder and milder and then it become almost fix. For checking of density, should I use from formula: d=m/v? You already have the density value; you posted it before. -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 listgmx-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
