Re: [gmx-users] Re:problem with simulation of freezing of water
On 11/11/12 11:22 AM, Ali Alizadeh wrote: Dear Justin Thank you for reply, I want to simulation of water freezing, my condition: pressure=300 bar and T=240 k , number 1656, run time= 100ns, I can not see regular structure of ice by MD simulation or by gromacs? In your opinion, if i want this structure of ice for my simulation, What can i do? Start by searching the literature for a suitable protocol. Ice simulations have been done before. As I said before, each water model has a different melting point, and hardly any of them correspond to the actual experimental value. See if you can produce a suitable simulation with a pressure of 1 bar (proof of concept) and then change conditions. What you have to keep in mind is that most water models were designed to work at ambient conditions for normal simulations. They do not necessarily work under extremes or produce useful results under those conditions. -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] Re:problem with simulation of freezing of water
On 2012-11-11 17:26, Justin Lemkul wrote: On 11/11/12 11:22 AM, Ali Alizadeh wrote: Dear Justin Thank you for reply, I want to simulation of water freezing, my condition: pressure=300 bar and T=240 k , number 1656, run time= 100ns, I can not see regular structure of ice by MD simulation or by gromacs? In your opinion, if i want this structure of ice for my simulation, What can i do? Start by searching the literature for a suitable protocol. Ice simulations have been done before. As I said before, each water model has a different melting point, and hardly any of them correspond to the actual experimental value. See if you can produce a suitable simulation with a pressure of 1 bar (proof of concept) and then change conditions. What you have to keep in mind is that most water models were designed to work at ambient conditions for normal simulations. They do not necessarily work under extremes or produce useful results under those conditions. -Justin Try TIP4P/Ice -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Re:problem with simulation of freezing of water
Hi, Also note that it is difficult to simulate the right structure of ice (Ih). You didn't write what you want to study, but search the literature carefully. You may need to use an ab-initio model. Ran Message: 7 Date: Sun, 11 Nov 2012 11:26:19 -0500 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Re:problem with simulation of freezing of water To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 509fd1ab.50...@vt.edu Content-Type: text/plain; charset=UTF-8; format=flowed On 11/11/12 11:22 AM, Ali Alizadeh wrote: Dear Justin Thank you for reply, I want to simulation of water freezing, my condition: pressure=300 bar and T=240 k , number 1656, run time= 100ns, I can not see regular structure of ice by MD simulation or by gromacs? In your opinion, if i want this structure of ice for my simulation, What can i do? Start by searching the literature for a suitable protocol. Ice simulations have been done before. As I said before, each water model has a different melting point, and hardly any of them correspond to the actual experimental value. See if you can produce a suitable simulation with a pressure of 1 bar (proof of concept) and then change conditions. What you have to keep in mind is that most water models were designed to work at ambient conditions for normal simulations. They do not necessarily work under extremes or produce useful results under those conditions. -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! End of gmx-users Digest, Vol 103, Issue 52 ** -- 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
