[gmx-users] difference in Coulomb SR and Coulomb 14?
Dear experts, Can you please make me understand the actual difference between Coulomb SR and Coulomb 14? -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- 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] Segmentation fault
Dear Gromacs Experts, I am having problem in execution of a command in Gromacs, thats when i use dssp for secondary structure analysis. it gives error: Reading file md_0_10.tpr, VERSION 4.5.5 (single precision) Reading file md_0_10.tpr, VERSION 4.5.5 (single precision) Segmentation fault (core dumped) saba@linuxserver:~/complex/MD I used the command : ulimit -s unlimited ulimit -c unlimited but no vain, the problem still persists, Tell me how to fix it? I urgently need to study secondary structure during simulations Thanks... -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- 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] Coulomb Energy
Dear Gromacs experts, I want to ask about coulomb energies. Like if coulomb-SR and coulomb-14 show high RMSD then what should we interpret from such results?? Average Coulomb Energy (kJ/mol) -1.62657e+06 RMSD 2236.85 Error Estimation 150 Total drift (kJ/mol) -894.82 Many thanks -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- 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] Coulomb Energies
Dear Gromacs experts, I want to ask about coulomb energies. Like if coulomb-SR and coulomb-14 show high RMSD then what should we interpret from such results?? Average Coulomb Energy (kJ/mol) -1.62657e+06 RMSD 2236.85 Error Estimation 150 Total drift (kJ/mol) -894.82 Many thanks -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- 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] I want only coordinates in md.xtc/md.pdb
Dear Sir, I need to ask you that if I want only pdb coordinates in the resultant md-noPBC.xtc/md-noPBC.pdb file rather than the solvant atoms and coordinates then what should I do. because the water box causes very delay in loading of frames and its difficult to viualize the trajectory. kindly help me to get out of the broblem. I only want that my protein get display in vmd rather than the water box. the size of md-noPBC.xtc is 612 Mb md-noPBC.pdb is 13.2 GB analysis is getting very slow and system is hanging. kindly help me out to fix this problem. Regards Thanks -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- 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] Analysis of Protein Complex
Dear Sir, I am studying a protein complex. I have perforemed 10ns simulations. I saved snapshots every10ps. sp all snap shopts I got were 1000. Now I want to analyse them with respect to interactions. I want to check the binding surfaces and binding points which come closer and incontact during simulations. Can you devise me a way to perform such kind of analysis. Further more I am interested to know the binding energies as well. What sort of other analysis can be done on this complex. -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- 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] frames in 2 trajectory files
Dear Gromacs group, I was running simulation of protein complex, due to power outage, my simulation got interrupted. I resumed it by the mdrun command provided. it got resumed starting from the frame, it stopped. Now simulation's all steps have been completed. but half frames are in one trajectory file while rest are in other which was created after resume. for analysis purpose I want all frames in one trajectory file. Can you tell me the way of doing so? waiting anxiously for help from your side. Thanks with anticipation Best Regards -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- 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] restoration of crashed simulation
Dear Justin, I have been simulation a protein complex on 10ns. about 4100,000/5000,000 of nsteps had been completed that my system got off due to electric cut-off. Now I want to resume this simulation. Is it possible to resume from the step it got ceased. Can you please tell me the proper command for the restoration? As this simulation was running since 6 days and I cant afford to restart it from the beginning:( Kindly tell me the full command to get it start from where it was stopped. Many thanks Regards -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- 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] Increasing time for simulation
Dear Justin, I am very sorry for a very basic question as i am beginner in Gromacs. Kindly do tell me that how can I increase time for the simulation. like 1st time i ran experiment on 1ns now i want to increase the time. kindly tell me that how can I do it and also tell that for a protein complex simulation, how much time would be enough to study the system in a good way as you told that 1ns is very short to study such type of system. many thanks -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- 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] Protein Complex simulation
Dear Justin, I need to ask you that when we simulate 2 proteins and if the md.trr show both protein quite far then what can be inferred from this when the complex was simulated for 1ns. thanks with anticipation Regards -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- 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] Strange problem.complex out of Box after EM
Dear Gromacs users I am trying to simulate a protein complex. That complex has been obtained after protein-protein docking. I have geneated topology, defined box and solvate, added ions successfully. My complex is centered in box. but when I performed Energy minimization then my protein complex comes out of box from one side. can any body help me in fixing this problem so that i could proceed towards equilibrium steps.. Many thanks with anticipation Regards Saba -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- 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
