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

[ZHANG Cheng]

Dear Qinghua,
Thank you very much.


Do you mean set "nstvout" and "nstenergy" as 0?


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


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