[gmx-users] How to run MD with longer recording interval to reduce the file size?
Qinghua Liao
scorpio.liao at gmail.com
Fri Dec 15 14:50:21 CET 2017
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
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