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

[Qinghua Liao]

Hello,

> Thank you Justin and Qinghua!
> Can I ask
> 1) I could not find "nstfout" (forces) in the md.mdp file from the tutorial. Should I add a new line of "nstfout=0"?
Yeah, you can add that line, or you can leave it be, the default is set 
as ZERO.
> 2) should I change "nstxout-compressed=5000" to "nstxout-compressed=50000"?
It depends on how many configurations you want to write out. 50000 might 
be a little to big if you just run short simulations.
> 3) Do you mean using "compressed-x-grps=Protein" will set xtc-grps as a
> group without waters and counterions?
This also depends on what system you are simulating. If it is a protein 
system, then it should be OK, if it is a protein+ ligand
or protein + DNA system, then you need to make the index file yourself 
with gmx make_ndx.


Best,
Qinghua
>
>
>
>
>
> ------------------ Original ------------------
> From:  "ZHANG Cheng";<272699575 at qq.com>;
> Date:  Fri, Dec 15, 2017 08:34 PM
> To:  "ZHANG Cheng"<272699575 at qq.com>;"gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
>
> Subject:  Re: How to run MD with longer recording interval to reduce the file size?
>
>
>
> 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