Re: [gmx-users] Using thermostats to create temperature gradient in system
Hi Agnivo, Temperature gradient means non-equilibrium MD (NEMD) See notes from Prof. Martini: https://nanohub.org/resources/7582/download/Martini_L10_NonequilibruimMD.pdf What observable would you like to measure? Lets say you want to measure observable A. One procedure I can think of: 1. You can run all system at T=300K with NVT. After equilibrium, continue running all system at T=400K with freezing solvent group. See, to how to freeze a group, http://manual.gromacs.org/online/mdp_opt.html#neq To get a good statistic, you need to repeat this procedure K times as solvent thermal wall configuration would be different at each simulation. 100ps? Where did you get that? You need to see how observable A behaves to see if 100ps is enough, A time average. And see how A behaves in K different cases. 2. Similar to previous procedure but this time after freezing solvent group, run system in NVE. Again, you need to repeat this many times to get a good statistic. Similarly monitor observable A to see if 500ps is enough. However, I suggest you to talk to someone having NEMD experience as this procedure is just a heuristic approach. -m -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using thermostats to create temperature gradient in system
Hi Agnivo; Yes, the idea of freezing the solvent or the protein in many times is to sample the non-equilibrium thermal process. It will remain in the target temperature on average, over many fixed configurations obtained by different NVT runs (equilibrium runs). But you may need to run this many K times to get a good statistic as I said. Concerning NVE, yes, do the same fixing approach with the protein. But as I mentioned earlier, this is quite heuristic approach, I suggest you to talk with any faculty member having background in non-equilibrium processes if this approach mimics what you need. Best, -m -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Silica Nanoparticles
You may try to use special potential designed for amorphous silica: A numerical investigation of the liquid–vapor coexistence curve of silica Yves Guissani and Bertrand Guillot J. Chem. Phys. 104, 7633 (1996) On 22 April 2014 17:12, Kazem Sepehrinia ksepehri...@gmail.com wrote: Hi Dear All, Have any of you guys prepared silica nanoparticles in your Molecular Simulation studies? I used some open databases for obtaining of bulk amorphous silica file. But i'm not able to prepare silica nanoparticles. Once again i used materials studio glasses and made a nanoparticle but that one is not working also. Because i tried to minimize it and job failed. Any help would be greatly appreciated. Thanks, Kazem Sepehrinia. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Computing melting point
Lindemann criterion might be easier. See For example, * Materials science: Melting from within Nature 413, 582-583 (11 October 2001) | doi:10.1038/35098169 Robert W. Cahn On 14 January 2014 15:35, Golshan Hejazi golshan.hej...@yahoo.com wrote: Hello everyone! I would like to compute the melting point of a drug crystalline system. In the literature, there exist a good number of methods to do so! Among them, I read Gibbs-Duhem integration technique in which one needs to provide a reference coexistence of solid/liquid. I read some articles in which they studied the melting point of water and also some ionic crystals. But I would like to know whether you can suggest me some more materials to read to find some ideas how to choose the reference structure for drug crystals? At the end, I would like to perform this simulation using gromacs. So if you think there are other methods which are more straight forward, would be great to let me know. Best G. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
