[gmx-users] doubt in mdrun

[Pablo Englebienne]

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* p.englebienne at tudelft.nl <mailto:p.englebienne at tudelft.nl>

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