Re: [gmx-users] SWM4_DP water on graphite surface
On 28/04/2012 3:33 AM, Ho, Tuan A. wrote: Dear Gromacs users, I would like to simulate a thin film of SWM4_DP water on graphite surface. First, I equilibrate the water only (run very well), then I add a graphite surface on it. I freeze the graphite surface but the graphite surface acted crazily after a few time step (graphite surface deform critically, blow). The error is Step 140: The charge group starting at atom 266 moved than the distance allowed by the domain decomposition (1.00) in direction Z distance out of cell 1.038218 Old coordinates:0.1232.6276.000 New coordinates:0.0130.671 11.038 Old cell boundaries in direction Z:5.978 10.000 New cell boundaries in direction Z:5.660 10.000 --- Program mdrun, VERSION 4.0.7 Source code file: domdec.c, line: 3654 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated I don't understand why I freeze the graphite surface but the carbon atom moved around. If it is because of bad contact, I think the water should be blown instead of carbon atom I ran the SPC/E water model on graphite very well. Probably you didn't use freezedim on the SOL degrees of freedom when you used that water model, as you have here. Mark I attached the mdp file, the topology file. Please let me know if I did anything wrong. Thanks in advance. Tuan. -- 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] SWM4_DP water on graphite surface
Thank Mark, I freeze the SOL because I would like to check if it is because of SOL bad contact. However, it turns out that the graphite deformation is the problem. My friend asks me to use only one processor, and it is running well (no SOL freeze). Hopefully, after I got the final configuration for serial run, I will be able to perform a parallel simulation. Thank you so much. Any idea for this problem is highly appreciated since I am not sure if I will be able to perform a parallel job. Tuan. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Friday, April 27, 2012 6:36 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] SWM4_DP water on graphite surface On 28/04/2012 3:33 AM, Ho, Tuan A. wrote: Dear Gromacs users, I would like to simulate a thin film of SWM4_DP water on graphite surface. First, I equilibrate the water only (run very well), then I add a graphite surface on it. I freeze the graphite surface but the graphite surface acted crazily after a few time step (graphite surface deform critically, blow). The error is Step 140: The charge group starting at atom 266 moved than the distance allowed by the domain decomposition (1.00) in direction Z distance out of cell 1.038218 Old coordinates:0.1232.6276.000 New coordinates:0.0130.671 11.038 Old cell boundaries in direction Z:5.978 10.000 New cell boundaries in direction Z:5.660 10.000 --- Program mdrun, VERSION 4.0.7 Source code file: domdec.c, line: 3654 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated I don't understand why I freeze the graphite surface but the carbon atom moved around. If it is because of bad contact, I think the water should be blown instead of carbon atom I ran the SPC/E water model on graphite very well. Probably you didn't use freezedim on the SOL degrees of freedom when you used that water model, as you have here. Mark I attached the mdp file, the topology file. Please let me know if I did anything wrong. Thanks in advance. Tuan. -- 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] SWM4_DP water on graphite surface
On 28/04/2012 10:54 AM, Ho, Tuan A. wrote: Thank Mark, I freeze the SOL because I would like to check if it is because of SOL bad contact. You can't do a dynamical simulation with zero degrees of freedom. However, it turns out that the graphite deformation is the problem. Under what conditions? Your earlier simulation probably blew up because of the above. Mark My friend asks me to use only one processor, and it is running well (no SOL freeze). Hopefully, after I got the final configuration for serial run, I will be able to perform a parallel simulation. Thank you so much. Any idea for this problem is highly appreciated since I am not sure if I will be able to perform a parallel job. Tuan. *From:*gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Mark Abraham *Sent:* Friday, April 27, 2012 6:36 PM *To:* Discussion list for GROMACS users *Subject:* Re: [gmx-users] SWM4_DP water on graphite surface On 28/04/2012 3:33 AM, Ho, Tuan A. wrote: Dear Gromacs users, I would like to simulate a thin film of SWM4_DP water on graphite surface. First, I equilibrate the water only (run very well), then I add a graphite surface on it. I freeze the graphite surface but the graphite surface acted crazily after a few time step (graphite surface deform critically, blow). The error is Step 140: The charge group starting at atom 266 moved than the distance allowed by the domain decomposition (1.00) in direction Z distance out of cell 1.038218 Old coordinates:0.1232.6276.000 New coordinates:0.0130.671 11.038 Old cell boundaries in direction Z:5.978 10.000 New cell boundaries in direction Z:5.660 10.000 --- Program mdrun, VERSION 4.0.7 Source code file: domdec.c, line: 3654 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated I don't understand why I freeze the graphite surface but the carbon atom moved around. If it is because of bad contact, I think the water should be blown instead of carbon atom I ran the SPC/E water model on graphite very well. Probably you didn't use freezedim on the SOL degrees of freedom when you used that water model, as you have here. Mark I attached the mdp file, the topology file. Please let me know if I did anything wrong. Thanks in advance. Tuan. -- 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] SWM4_DP water on graphite surface
Thank Mark, I did not freeze the SOL. My graphite surface blew up. The system is: A water film is about 6A from graphite surface. The water film is equilibrated before placed on graphite surface. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Friday, April 27, 2012 8:02 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] SWM4_DP water on graphite surface On 28/04/2012 10:54 AM, Ho, Tuan A. wrote: Thank Mark, I freeze the SOL because I would like to check if it is because of SOL bad contact. You can't do a dynamical simulation with zero degrees of freedom. However, it turns out that the graphite deformation is the problem. Under what conditions? Your earlier simulation probably blew up because of the above. Mark My friend asks me to use only one processor, and it is running well (no SOL freeze). Hopefully, after I got the final configuration for serial run, I will be able to perform a parallel simulation. Thank you so much. Any idea for this problem is highly appreciated since I am not sure if I will be able to perform a parallel job. Tuan. From: gmx-users-boun...@gromacs.orgmailto:gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Friday, April 27, 2012 6:36 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] SWM4_DP water on graphite surface On 28/04/2012 3:33 AM, Ho, Tuan A. wrote: Dear Gromacs users, I would like to simulate a thin film of SWM4_DP water on graphite surface. First, I equilibrate the water only (run very well), then I add a graphite surface on it. I freeze the graphite surface but the graphite surface acted crazily after a few time step (graphite surface deform critically, blow). The error is Step 140: The charge group starting at atom 266 moved than the distance allowed by the domain decomposition (1.00) in direction Z distance out of cell 1.038218 Old coordinates:0.1232.6276.000 New coordinates:0.0130.671 11.038 Old cell boundaries in direction Z:5.978 10.000 New cell boundaries in direction Z:5.660 10.000 --- Program mdrun, VERSION 4.0.7 Source code file: domdec.c, line: 3654 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated I don't understand why I freeze the graphite surface but the carbon atom moved around. If it is because of bad contact, I think the water should be blown instead of carbon atom I ran the SPC/E water model on graphite very well. Probably you didn't use freezedim on the SOL degrees of freedom when you used that water model, as you have here. Mark I attached the mdp file, the topology file. Please let me know if I did anything wrong. Thanks in advance. Tuan. -- 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
