[gmx-users] How to run MD with longer recording interval to reduce the file size?

[Justin Lemkul]

On 12/15/17 7:34 AM, ZHANG Cheng wrote:
> Dear Qinghua,
> Thank you very much.
>
>
> Do you mean set "nstvout" and "nstenergy" as 0?

nstenergy is the frequency of writing energy terms to the .edr file. It 
has no effect on the .trr, which is only impacted by nstxout 
(coordinates), nstvout (velocities), and nstfout (forces).

>
> Also, how to set xtc-grps as a group?

It's compressed-x-grps.

-Justin

>
> The original md.mdp file is:
>
>
> title		= OPLS MD simulation
> ; Run parameters
> integrator	= md		; leap-frog integrator
> nsteps		= 100000000	; 2 * 100000000 = 200000000 fs = 200 ns
> dt		    = 0.002		; 2 fs
> ; Output control
> nstxout		        = 5000		; save coordinates every 10 ps
> nstvout		        = 5000		; save velocities every 10 ps
> nstenergy	        = 5000		; save energies every 10 ps
> nstlog		        = 5000		; update log file every 10 ps
> nstxout-compressed  = 5000      ; save compressed coordinates every 10 ps
>                                  ; nstxout-compressed replaces nstxtcout
> compressed-x-grps   = System    ; replaces xtc-grps
> ; 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
> cutoff-scheme   = Verlet
> ns_type		    = grid		; search neighboring grid cells
> nstlist		    = 10	    ; 20 fs, largely irrelevant with Verlet scheme
> 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		= 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
>
>
>
>
>
>
>
> ------------------ Original ------------------
> From:  "ZHANG Cheng";<272699575 at qq.com>;
> Date:  Fri, Dec 15, 2017 06:33 PM
> To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
> Cc:  "ZHANG Cheng"<272699575 at qq.com>;
> Subject:  How to run MD with longer recording interval to reduce the file size?
>
>
>
> Dear Gromacs,
> I am following Justin's tutorial of "Lysozyme in Water" to run the MD.
>
>
> The .trr file got more than 10 GB after 30 ns. So I plan to run a MD with less frequent intervals.
>
>
> In the md.mdp file, the "dt = 0.002". My understanding is to change the five "5000" into "50000" to achieve 10 times less file size:
>
>
> i.e. change the following
> nstxout		        = 5000
> nstvout		        = 5000
> nstenergy	        = 5000
> nstlog		        = 5000
> nstxout-compressed  = 5000
>
>
>
> into
>
>
> nstxout		        = 50000
> nstvout		        = 50000
> nstenergy	        = 50000
> nstlog		        = 50000
> nstxout-compressed  = 50000
>
>
>
> Can I ask, if there is something else I need to do in addition to those five "5000"?
>
>
> Thank you.
>
>
> Yours sincerely
> Cheng

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Virginia Tech Department of Biochemistry

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