[gmx-users] xtc file and trr file
acootbrett at yahoo.com
Fri Aug 17 22:33:13 CEST 2012
Follwong is the MD mdp file I used for my production MD, which I downloaded from http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/md.mdp.
Clearly it writes how it extract xtp file. Will you please explain to me which is the command for the extraction of trr file? And based on which command we can know by VMD the xtc file will have more frames in comparison with the trr file?
title = OPLS Lysozyme MD
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 500000 ; 2 * 500000 = 1000 ps, 1 ns
dt = 0.002 ; 2 fs
; Output control
nstxout = 1000 ; save coordinates every 2 ps
nstvout = 1000 ; save velocities every 2 ps
nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps
nstenergy = 1000 ; save energies every 2 ps
nstlog = 1000 ; update log file every 2 ps
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off
----- Forwarded Message -----
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Friday, 17 August 2012 8:41 PM
Subject: Re: [gmx-users] xtc file and trr file
On 17/08/2012 6:46 PM, Acoot Brett wrote:
> Dear All,
> After a production MD, both the xtc file and trr file are produced. trr file is much larger than the xtc file. But when we openned the original gro file one of the file from xtc file and trr file in VMD, we will find the xtc contains more frames in comparison with the trr file.
> Will you please explain why xtc file is smaller file than the trr file, but the xtc file contains more frames in VMD?
Clearly one format is more efficient at storing frames than the other. They have different numbers of frames because that's what you asked for in your .mdp file (unless you've post-processed).
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