Hi Shine,
The amount of data is due to a very long simulation (1 microsecond!)
coupled to a very frequent dumping of snapshots (every 1000 frames).
You should question whether you need such frequent storage of the
trajectory (e.g., for analysis of diffusion) or if less frequent will do
just fine. Also, question whether you need such a long simulation or a
shorter one would be sufficient.
In any case, you could do a shorter run, analyze the trajectory and
continue the simulation as described in
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations .
Cheers,
Pablo
Dr. Pablo Englebienne
Postdoctoral Researcher
*TU Delft / 3mE / Process & Energy*
/Engineering Thermodynamics (ETh) group/
Building 46
Leeghwaterstraat 44, room 030
2628 CA Delft
The Netherlands
*T* +31 (0)15 27 86662 <tel:+31152786662>
*E* [email protected] <mailto:[email protected]>
On 05/01/2013 07:29 AM, Shine A wrote:
Sir,
I studying the dynamics of a peptide in explicit solvent model.But
during the mdrun I got the message like this.
NOTE 1 [file md.mdp]:
This run will generate roughly 1177130 Mb of data
why the run generating this much amount of data?
The md.mdp file I used is shown below
title = OPLS Lysozyme MD
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 500000000 ; 2 * 500000000 = 1000000 ps, 1000 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
; Neighborsearching
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)
; Electrostatics
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 = 320 320 ; 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
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