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.
