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";<272699...@qq.com>; Date: Fri, Dec 15, 2017 06:33 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.