Aw: Re: [gmx-users] air-water-interface
I was under the impression a vacumn, or even gas/liquid interface becomes uniform molecule wise in such simulations due to scale. Thus, the applied pressure and other corrections necessary to set up the interface on a small scale, such as caclulated force at an imaginary interface for given gas/liquid systems? I wounder though, is it possible to give the pressure corrections a direction (a single wall instead of the entire unit cell)? Gesendet:Montag, 13. Mai 2013 um 14:16 Uhr Von:Nawel Mele nawel.m...@gmail.com An:Discussion list for GROMACS users gmx-users@gromacs.org Betreff:Re: [gmx-users] air-water-interface Thanks a lot for your answer. So by increasing the z coordinate after solvated the system we induce creation of a empty space above the solvated box. After minimisation a few water molecules move above its new empty space because their link are not strong enough. 2013/5/13 Justin Lemkul jalem...@vt.edu On 5/13/13 8:01 AM, Nawel Mele wrote: So we just compute an interface vacuum-water like the picture in attach in increase the coordinate value of the z-axis of the box? The list does not accept attachments. If you want to post an image or file, provide a public link to access it. BUt I dont understand how just like that we creat an empty place and water move to this place?? Seems like intuitive behavior to me. Think about basic physics and thermodynamics. -Justin 2013/5/13 Justin Lemkul jalem...@vt.edu On 5/13/13 6:10 AM, Nawel Mele wrote: Hi all, I am performing a simulation of protein at air/water interface. For create an air-water interface I just expand the box in the z direction. So,aAfter minimization we can noticed that water molecules moved out of bulk water in the z direction. Why you just need to expand the z-axis for obtain this interface?? I dont understand the mechanism. Youre not creating an air-water interface by doing this, youre creating an vacuum-water interface and your water molecules are evaporating into the empty space. -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/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *Mlle* Mele Nawel Master 2 In Silico Drug Design University of Paris Diderot/Strasbourg -- 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 dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant 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
[gmx-users] air-water-interface
Hi all, I am performing a simulation of protein at air/water interface. For create an air-water interface I just expand the box in the z direction. So,aAfter minimization we can noticed that water molecules moved out of bulk water in the z direction. Why you just need to expand the z-axis for obtain this interface?? I don't understand the mechanism. Thanks a lot for your answer -- *Mlle* Mele Nawel Master 2 In Silico Drug Design University of Paris Diderot/Strasbourg -- 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] air-water-interface
On 5/13/13 6:10 AM, Nawel Mele wrote: Hi all, I am performing a simulation of protein at air/water interface. For create an air-water interface I just expand the box in the z direction. So,aAfter minimization we can noticed that water molecules moved out of bulk water in the z direction. Why you just need to expand the z-axis for obtain this interface?? I don't understand the mechanism. You're not creating an air-water interface by doing this, you're creating an vacuum-water interface and your water molecules are evaporating into the empty space. -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] air-water-interface
So we just compute an interface vacuum-water like the picture in attach in increase the coordinate value of the z-axis of the box? BUt I don't understand how just like that we creat an empty place and water move to this place?? 2013/5/13 Justin Lemkul jalem...@vt.edu On 5/13/13 6:10 AM, Nawel Mele wrote: Hi all, I am performing a simulation of protein at air/water interface. For create an air-water interface I just expand the box in the z direction. So,aAfter minimization we can noticed that water molecules moved out of bulk water in the z direction. Why you just need to expand the z-axis for obtain this interface?? I don't understand the mechanism. You're not creating an air-water interface by doing this, you're creating an vacuum-water interface and your water molecules are evaporating into the empty space. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *Mlle* Mele Nawel Master 2 In Silico Drug Design University of Paris Diderot/Strasbourg -- 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] air-water-interface
On 5/13/13 8:01 AM, Nawel Mele wrote: So we just compute an interface vacuum-water like the picture in attach in increase the coordinate value of the z-axis of the box? The list does not accept attachments. If you want to post an image or file, provide a public link to access it. BUt I don't understand how just like that we creat an empty place and water move to this place?? Seems like intuitive behavior to me. Think about basic physics and thermodynamics. -Justin 2013/5/13 Justin Lemkul jalem...@vt.edu On 5/13/13 6:10 AM, Nawel Mele wrote: Hi all, I am performing a simulation of protein at air/water interface. For create an air-water interface I just expand the box in the z direction. So,aAfter minimization we can noticed that water molecules moved out of bulk water in the z direction. Why you just need to expand the z-axis for obtain this interface?? I don't understand the mechanism. You're not creating an air-water interface by doing this, you're creating an vacuum-water interface and your water molecules are evaporating into the empty space. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] air-water-interface
Thanks a lot for your answer. So by increasing the z coordinate after solvated the system we induce creation of a empty space above the solvated box. After minimisation a few water molecules move above its new empty space because their link are not strong enough. 2013/5/13 Justin Lemkul jalem...@vt.edu On 5/13/13 8:01 AM, Nawel Mele wrote: So we just compute an interface vacuum-water like the picture in attach in increase the coordinate value of the z-axis of the box? The list does not accept attachments. If you want to post an image or file, provide a public link to access it. BUt I don't understand how just like that we creat an empty place and water move to this place?? Seems like intuitive behavior to me. Think about basic physics and thermodynamics. -Justin 2013/5/13 Justin Lemkul jalem...@vt.edu On 5/13/13 6:10 AM, Nawel Mele wrote: Hi all, I am performing a simulation of protein at air/water interface. For create an air-water interface I just expand the box in the z direction. So,aAfter minimization we can noticed that water molecules moved out of bulk water in the z direction. Why you just need to expand the z-axis for obtain this interface?? I don't understand the mechanism. You're not creating an air-water interface by doing this, you're creating an vacuum-water interface and your water molecules are evaporating into the empty space. -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/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *Mlle* Mele Nawel Master 2 In Silico Drug Design University of Paris Diderot/Strasbourg -- 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] air-water interface
Dear Gromacs Specialists, I want to make a system consists of one box of solvent (for example water) that there is 100 surfactant molecules in it and water is in contact with air in surface as same as we do in laboratory in beaker. But I don't know how should I define this air-water interface for my system. Please help me. Thanks in advance. Best Regards Sara -- 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] air-water interface
Search the literature and see what others have done to do exactly this. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of mohammad agha Sent: Tuesday, 21 February 2012 8:04 PM To: Discussion list for GROMACS users Subject: [gmx-users] air-water interface Dear Gromacs Specialists, I want to make a system consists of one box of solvent (for example water) that there is 100 surfactant molecules in it and water is in contact with air in surface as same as we do in laboratory in beaker. But I don't know how should I define this air-water interface for my system. Please help me. Thanks in advance. Best Regards Sara -- 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] air-water interface
Hi, everyone I find that i used T and P coupling in water-air interface, that is the reason my system imploded. So i changed to NVT. But there are still fatal errors. I have some questions concerning .gro file. for example in spc216.gro, there are both + and - psotions. But in other .gro file, all is + postion. What is the difference between .gro ? Thanks -- 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] air-water interface
On 2/12/2010 12:30 AM, 铁锋 彭 wrote: Hi, everyone I find that i used T and P coupling in water-air interface, that is the reason my system imploded. So i changed to NVT. But there are still fatal errors. I have some questions concerning .gro file. for example in spc216.gro, there are both + and - psotions. But in other .gro file, all is + postion. What is the difference between .gro ? If the system is periodic, what does the sign matter? 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
