[gmx-users] water genbox 3x3x0.8 EM not successful T not high
Hi, I want to simulate 3x3x0.8 water film (bulk water) first creat the water, genbox -cs -o film.gro -box 3 3 0.8 then, i EM the bulk water; Using steep, but t = 0.011 ps: Water molecule starting at atom 298 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates then i run, and i get the result. I use NPT, and T=300K. I run several times, but the final T was still 411K. So what could i do to get EM process successful? And what is the reason ? why i can not control the T 300K? Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -9496.38136.145135.455 -0.158085 -47.4256 Kinetic En. 2358.273.587673.5471 -0.0281891 -8.45676 Total Energy -7138.19136.284135.326 -0.186274 -55.8824 Temperature 411.94512.854812.8477 -0.00492426 -1.47728 Pressure (bar) -1.66406704.355704.355 -0.00424907 -1.27473 Box-X 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Y 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Z 0.778108 0.00343907 0.00343437 -2.07536e-06 -0.000622609 Density (SI) 1038.713.616513.5998 0.007785132.33555 Heat Capacity Cv:12.49 J/mol K (factor = 0.000973754) -- 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] water genbox 3x3x0.8 EM not successful T not high
Could you please attach your minimization parameters (mdp file) and grompp/mdrun commands? Your simulation box seems a bit strange for me. If you're using periodic boundary conditions you have not a thin film, but an infinite bulk water (remember pbc replicate the box in all directions). With such a small Z axis you might have probles with the cut-off radius being longer than a particle image. Javier El 16/12/10 10:38, gromacs escribió: Hi, I want to simulate 3x3x0.8 water film (bulk water) first creat the water, genbox -cs -o film.gro -box 3 3 0.8 then, i EM the bulk water; Using steep, but t = 0.011 ps: Water molecule starting at atom 298 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates then i run, and i get the result. I use NPT, and T=300K. I run several times, but the final T was still 411K. So what could i do to get EM process successful? And what is the reason ? why i can not control the T 300K? Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -9496.38 136.145 135.455 -0.158085 -47.4256 Kinetic En. 2358.2 73.5876 73.5471 -0.0281891 -8.45676 Total Energy -7138.19 136.284 135.326 -0.186274 -55.8824 Temperature 411.945 12.8548 12.8477 -0.00492426 -1.47728 Pressure (bar) -1.66406 704.355 704.355 -0.00424907 -1.27473 Box-X 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Y 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Z 0.778108 0.00343907 0.00343437 -2.07536e-06 -0.000622609 Density (SI)nbs p; 1038.7 13.6165 13.5998 0.00778513 2.33555 Heat Capacity Cv: 12.49 J/mol K (factor = 0.000973754) -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Química-Física Universidad de Murcia 30100 MURCIA (España) Tlf.(+34)868887434 -- 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] water genbox 3x3x0.8 EM not successful T not high
On 12/16/10, Javier Cerezo j...@um.es wrote: Could you please attach your minimization parameters (mdp file) and grompp/mdrun commands? Your simulation box seems a bit strange for me. If you're using periodic boundary conditions you have not a thin film, but an infinite bulk water (remember pbc replicate the box in all directions). With such a small Z axis you might have probles with the cut-off radius being longer than a particle image. GROMACS enforces the minimum-image convention, so we can deduce that that rcoulomb was unreasonably short. El 16/12/10 10:38, gromacs escribió: Hi, I want to simulate 3x3x0.8 water film (bulk water) first creat the water, genbox -cs -o film.gro -box 3 3 0.8 then, i EM the bulk water; Using steep, but t = 0.011 ps: Water molecule starting at atom 298 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Here's the first hint something is wrong. Don't ignore it and plow on! then i run, and i get the result. I use NPT, and T=300K. I run several times, but the final T was still 411K. So what could i do to get EM process successful? And what is the reason ? why i can not control the T 300K? Over what timescale did you equilibrate? Over what *separate* timescale did you observe? Mark Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -9496.38 136.145 135.455 -0.158085 -47.4256 Kinetic En. 2358.2 73.5876 73.5471 -0.0281891 -8.45676 Total Energy -7138.19 136.284 135.326 -0.186274 -55.8824 Temperature 411.945 12.8548 12.8477 -0.00492426 -1.47728 Pressure (bar) -1.66406 704.355 704.355 -0.00424907 -1.27473 Box-X 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Y 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Z 0.778108 0.00343907 0.00343437 -2.07536e-06 -0.000622609 Density (SI)nbs p; 1038.7 13.6165 13.5998 0.00778513 2.33555 Heat Capacity Cv: 12.49 J/mol K (factor = 0.000973754) -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Química-Física Universidad de Murcia 30100 MURCIA (España) Tlf.(+34)868887434 -- 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. 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
[gmx-users] water genbox 3x3x0.8 EM not successful T too high
Message: 3 Date: Thu, 16 Dec 2010 11:50:51 -0500 From: Vitaly Chaban vvcha...@gmail.com Subject: [gmx-users] Re: water genbox 3x3x0.8 EM not successful T not high To: gmx-users@gromacs.org Cc: gromacs ptf1...@163.com Message-ID: aanlktikykv=-oev10bxgys5n_nmqxbonwbhxkybuh...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 From: gromacs ptf1...@163.com Subject: [gmx-users] water genbox 3x3x0.8 EM not successful T not high Hi, I want to simulate 3x3x0.8 water film (bulk water) first creat the water, genbox -cs -o film.gro -box 3 3 0.8 then, i EM the bulk water; Using steep, but t = 0.011 ps: Water molecule starting at atom 298 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates then i run, and i get the result. I use NPT, and T=300K. I run several times, but the final T was still 411K. So what could i do to get EM process successful? And what is the reason ? why i can not control the T 300K? Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -9496.38136.145135.455 -0.158085 -47.4256 Kinetic En. 2358.273.587673.5471 -0.0281891 -8.45676 Total Energy -7138.19136.284135.326 -0.186274 -55.8824 Temperature 411.94512.854812.8477 -0.00492426 -1.47728 Pressure (bar) -1.66406704.355704.355 -0.00424907 -1.27473 Box-X 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Y 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Z 0.778108 0.00343907 0.00343437 -2.07536e-06 -0.000622609 Density (SI) 1038.713.616513.5998 0.00778513 2.33555 Heat Capacity Cv:12.49 J/mol K (factor = 0.000973754) Hey, gromacs - Nice to hear from you here... It is a bad idea to simulate something with any cartesian dimension lower than a couple of nanometers using classical FFs. All your problems are generated by 0.8 nm of the z-side. -- Dr. Vitaly V. Chaban Rochester, U.S.A. -- Thanks very much. I use the cutoff=0.38, because the cutoff should be smaller than the half box size. I guess it may be the Z dimension is too small, Plus the PBC. But when i use 1.8x1.8x1.8nm bulk water, all results are OK. My teacher wants me to simulate 3x3x0.8, 3x3x0.9 nm water film's rupture. So i have to run bulk 3x3x0.8 water and then add box to 3x3x9 to form interface. So if i want to run run bulk 3x3x0.8 water, how could i do? which FF should i use? the high T may be due to EM not success?? -- 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] water genbox 3x3x0.8 EM not successful T too high
Why can't you energy minimise the water block / film in the final box size? And you can't simply change the cut-offs like that to suit your box size, you need to use the settings that the forcefield was parameterised for, or what others have studied / published and found to be suitable. You can't swap and changes those settings at a whim. 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 gromacs Sent: Friday, 17 December 2010 11:32 AM To: gmx-users@gromacs.org Subject: [gmx-users] water genbox 3x3x0.8 EM not successful T too high Message: 3 Date: Thu, 16 Dec 2010 11:50:51 -0500 From: Vitaly Chaban vvcha...@gmail.com Subject: [gmx-users] Re: water genbox 3x3x0.8 EM not successful T not high To: gmx-users@gromacs.org Cc: gromacs ptf1...@163.com Message-ID: aanlktikykv=-oev10bxgys5n_nmqxbonwbhxkybuh...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 From: gromacs ptf1...@163.com Subject: [gmx-users] water genbox 3x3x0.8 EM not successful T not high Hi, I want to simulate 3x3x0.8 water film (bulk water) first creat the water, genbox -cs -o film.gro -box 3 3 0.8 then, i EM the bulk water; Using steep, but t = 0.011 ps: Water molecule starting at atom 298 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates then i run, and i get the result. I use NPT, and T=300K. I run several times, but the final T was still 411K. So what could i do to get EM process successful? And what is the reason ? why i can not control the T 300K? Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -9496.38136.145135.455 -0.158085 -47.4256 Kinetic En. 2358.273.587673.5471 -0.0281891 -8.45676 Total Energy -7138.19136.284135.326 -0.186274 -55.8824 Temperature 411.94512.854812.8477 -0.00492426 -1.47728 Pressure (bar) -1.66406704.355704.355 -0.00424907 -1.27473 Box-X 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Y 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Z 0.778108 0.00343907 0.00343437 -2.07536e-06 -0.000622609 Density (SI) 1038.713.616513.5998 0.00778513 2.33555 Heat Capacity Cv:12.49 J/mol K (factor = 0.000973754) Hey, gromacs - Nice to hear from you here... It is a bad idea to simulate something with any cartesian dimension lower than a couple of nanometers using classical FFs. All your problems are generated by 0.8 nm of the z-side. -- Dr. Vitaly V. Chaban Rochester, U.S.A. -- Thanks very much. I use the cutoff=0.38, because the cutoff should be smaller than the half box size. I guess it may be the Z dimension is too small, Plus the PBC. But when i use 1.8x1.8x1.8nm bulk water, all results are OK. My teacher wants me to simulate 3x3x0.8, 3x3x0.9 nm water film's rupture. So i have to run bulk 3x3x0.8 water and then add box to 3x3x9 to form interface. So if i want to run run bulk 3x3x0.8 water, how could i do? which FF should i use? the high T may be due to EM not success?? -- 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] water genbox 3x3x0.8 EM not successful T not high
Forwarding messages From: gromacs ptf1...@163.com Date: 2010-12-17 12:48:55To: vvcha...@gmail.com Cc: gmx-users@gromacs.org Subject: Re:Re: water genbox 3x3x0.8 EM not successful T not high OK. I will use your method. But i am afraid there will be something wrong. Because generally, i should run the 3x3x0.8 NPT water, and then i use editconf to add the water to 3x3x3. If i donot run 3x3x0.8, i may not be able to run the final interface box. Because the water in the box is not at proper situation or position. Anyway, i will have a try first. One problem is that how can i make the Energy Minimising successful? There are some water molecules not in suitable position. If i have problem or success, i will give an answer to all. At 2010-12-17 09:51:57，Vitaly Chaban vvcha...@gmail.com wrote: Hey, gromacs - Nice to hear from you here... It is a bad idea to simulate something with any cartesian dimension lower than a couple of nanometers using classical FFs. All your problems are generated by 0.8 nm of the z-side.-- Dr. Vitaly V. Chaban Rochester, U.S.A. Thanks very much. I use the cutoff=0.38, because the cutoff should be smaller than the half box size. I guess it may be the Z dimension is too small, Plus the PBC. But when i use 1.8x1.8x1.8nm bulk water, all results are OK. My teacher wants me to simulate 3x3x0.8, 3x3x0.9 nm water film's rupture. So i have to run bulk 3x3x0.8 water and then add box to 3x3x9 to form interface. So if i want to run run bulk 3x3x0.8 water, how could i do? which FF should i use? the high T may be due to EM not success?? I believe you use the term bulk water in another sense as compared to all other guys here. When people say bulk liquid they imply the endless ocean of this liquid. It is not important what particular side lengths you have, since due to PBC you get infinitively large system. I suspect your teacher wants you to obtain a film of water that would be about 3 molecular layers wide. That's easy. Take your current box of water and apply editconf - editconf -f current_conf -o water_film_conf -box 3 3 3 Finally, just start MD run with a water_film_conf. You'll have the same periodic box , but water molecules will be present only at its center surrounded by vacuum in one (Z) direction. Happy GROMACSing,Dr. Vitaly V. Chaban Rochester, U.S.A.-- 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
