Hi I have read throught the Appendix C. The following is the .mdp file.
Type the command g_energy -f abc-NVT500.edr -o abc-NVT500.xvg choose Pressure Based on my understanding of the Appendix C => g_energy will print out the instantaneous Pressure every 1000 step and save it into abc-NVT500.xvg. There are overall 250 instantaneous Pressure recorded. (overall steps = 250000=> 250000/1000=250) And, the average pressure is shown on the screen. the average pressure = (sum of the 250 instantanous pressure) / 250 Also , the value of RMSD Fluct. Drift Tot-Drift are also calculated from the 250 instantaneous pressure? Is anything wrong above ? Thank you Lin ; RUN CONTROL PARAMETERS integrator = md tinit = 0 ; Starting time dt = 0.002 ; 2 femtosecond time step for integration nsteps = 250000 ; 500 picoseconds total simulation time comm_mode = Linear ; Removing overall translations from the system nstcomm = 1 ; ... and doing so every step ; OUTPUT CONTROL OPTIONS nstxout = 1000 ; Writing full precision coordinates every nanosecond nstvout = 0 ; Writing velocities every nanosecond nstfout = 0 ; Not writing forces nstlog = 0 ; Writing to the log file every step nstenergy = 1000 ; Writing out energy information every step nstxtcout = 1000 ; Writing coordinates every step xtc_precision = 1000 ; Floating point number to integer scaling xtc-grps = System energygrps = Protein Non-Protein _______________________________________________ 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/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/mailing_lists/users.php
