[gmx-users] increase the time frame
Hi users, Iam running a minimization on protein complex in vacuum. i have set the parameters as following- ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title= Energy Minimization; Title of run ; The following line tell the program the standard locations where to find certain files cpp= /lib/cpp; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator= steepest; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1.0 kJ/mol emstep = 0.01 nsteps= 5; Maximum number of (minimization) steps to perform nstenergy= 1 ; Write energies to disk every nstenergy steps energygrps= Protein; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstxout = 1 nstlist= 10; Frequency to update the neighbor list and long range forces ns_type= grid ; Method to determine neighbor list (simple, grid) rlist= 1.0; Cut-off for making neighbor list (short range forces) coulombtype= cutoff ; Treatment of long range electrostatic interactions rcoulomb= 1.0; long range electrostatic cut-off rvdw= 1.4; long range Van der Waals cut-off constraints= none; Bond types to replace by constraints pbc= no; Periodic Boundary Conditions (yes/no) But from this i could write only 2 frames i need to increase the time frames, what is to be changed in the parameters. Thanks, Aiswarya -- 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] increase the time frame
On 21/10/2011 5:09 PM, aiswarya pawar wrote: Hi users, Iam running a minimization on protein complex in vacuum. i have set the parameters as following- ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title= Energy Minimization; Title of run ; The following line tell the program the standard locations where to find certain files cpp= /lib/cpp; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator= steepest; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1.0 kJ/mol emstep = 0.01 nsteps= 5; Maximum number of (minimization) steps to perform nstenergy= 1 ; Write energies to disk every nstenergy steps energygrps= Protein; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstxout = 1 nstlist= 10; Frequency to update the neighbor list and long range forces ns_type= grid ; Method to determine neighbor list (simple, grid) rlist= 1.0; Cut-off for making neighbor list (short range forces) coulombtype= cutoff ; Treatment of long range electrostatic interactions rcoulomb= 1.0; long range electrostatic cut-off rvdw= 1.4; long range Van der Waals cut-off constraints= none; Bond types to replace by constraints pbc= no; Periodic Boundary Conditions (yes/no) But from this i could write only 2 frames i need to increase the time frames, what is to be changed in the parameters. This will write every frame of the EM, but if it only has two steps... 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
Re: [gmx-users] increase the time frame
After running this minimization when i did gmxcheck i got this output trn version: GMX_trn_file (single precision) Reading frame 0 time9.000 # Atoms 4113 Reading frame 3 time 57.000 Timesteps at t=31 don't match (12, 26) Reading frame 4 time 69.000 Timesteps at t=57 don't match (26, 12) Reading frame 14 time 192.000 Timesteps at t=184 don't match (13, 8) Last frame 14 time 192.000 Item#frames Step15 Time15 Lambda 15 Coords 15 Velocities 0 Forces 0 Box 15 why is it saying that Timesteps at t=31 don't match (12, 26). On Fri, Oct 21, 2011 at 12:25 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 21/10/2011 5:09 PM, aiswarya pawar wrote: Hi users, Iam running a minimization on protein complex in vacuum. i have set the parameters as following- ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title= Energy Minimization; Title of run ; The following line tell the program the standard locations where to find certain files cpp= /lib/cpp; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator= steepest; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1.0 kJ/mol emstep = 0.01 nsteps= 5; Maximum number of (minimization) steps to perform nstenergy= 1 ; Write energies to disk every nstenergy steps energygrps= Protein; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstxout = 1 nstlist= 10; Frequency to update the neighbor list and long range forces ns_type= grid ; Method to determine neighbor list (simple, grid) rlist= 1.0; Cut-off for making neighbor list (short range forces) coulombtype= cutoff ; Treatment of long range electrostatic interactions rcoulomb= 1.0; long range electrostatic cut-off rvdw= 1.4; long range Van der Waals cut-off constraints= none; Bond types to replace by constraints pbc= no; Periodic Boundary Conditions (yes/no) But from this i could write only 2 frames i need to increase the time frames, what is to be changed in the parameters. This will write every frame of the EM, but if it only has two steps... Mark -- 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
