[gmx-users] how to check the intermediate coordinated even when the simulation is running
I am very new to this MD simulation, by reading the tutorials in the website I have run an simulation and it is running from last 5 day and I am not getting whether it is running properly or not. Could any one kindly tell me how to see whether the simulation is running or not and also how can I check the intermediate coordinated even when the simulation is running. Kindly help me. -- Ananya Chatterjee, -- 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] how to check the intermediate coordinated even when the simulation is running
Hi ananya, You can get the coordinates using trjconv: trjconv -f file.xtc -s file.tpr -o file.pdb -b initial time in ps -e final time in ps this will give you pdb at the time you have mentioned. For your first question- as far as I know you need to check whether there is any periodic image violation using g_mindist. Other things what you have to check depends on the parameter you want to see. Probably others may give a better answer regarding this. Bye kavya On Fri, Nov 9, 2012 at 5:04 PM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: I am very new to this MD simulation, by reading the tutorials in the website I have run an simulation and it is running from last 5 day and I am not getting whether it is running properly or not. Could any one kindly tell me how to see whether the simulation is running or not and also how can I check the intermediate coordinated even when the simulation is running. Kindly help me. -- Ananya Chatterjee, -- 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 -- 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] how to check the intermediate coordinated even when the simulation is running
On 11/9/12 7:06 AM, Kavyashree M wrote: Hi ananya, You can get the coordinates using trjconv: trjconv -f file.xtc -s file.tpr -o file.pdb -b initial time in ps -e final time in ps This is more easily accomplished with trjconv -dump. I would also advise making a copy of the .trr/.xtc file to be operated upon rather than trying to do I/O operations on a file that may be accessed by the simulation while it is running. this will give you pdb at the time you have mentioned. For your first question- as far as I know you need to check whether there is any periodic image violation using g_mindist. Other things what you have to check depends on the parameter you want to see. It depends on what the OP means by running properly. If one simply wants to ensure that the simulation is indeed going along, simply listing the files and looking at time stamps should tell you that, or following the content of the .log file using the Unix command tail. -Justin Probably others may give a better answer regarding this. Bye kavya On Fri, Nov 9, 2012 at 5:04 PM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: I am very new to this MD simulation, by reading the tutorials in the website I have run an simulation and it is running from last 5 day and I am not getting whether it is running properly or not. Could any one kindly tell me how to see whether the simulation is running or not and also how can I check the intermediate coordinated even when the simulation is running. Kindly help me. -- Ananya Chatterjee, -- 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
