[gmx-users] g_energy => both instantaneous and average
chihying2008 at gmail.com
Fri Jun 19 00:16:29 CEST 2009
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
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
(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 ?
; RUN CONTROL PARAMETERS
integrator = md
tinit = 0 ; Starting time
dt = 0.002 ; 2 femtosecond time step for
nsteps = 250000 ; 500 picoseconds total simulation time
comm_mode = Linear ; Removing overall translations from
nstcomm = 1 ; ... and doing so every step
; OUTPUT CONTROL OPTIONS
nstxout = 1000 ; Writing full precision coordinates
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
xtc-grps = System
energygrps = Protein Non-Protein
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