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";<272699...@qq.com>;
Date: Fri, Dec 15, 2017 08:34 PM
To: "ZHANG
Cheng"<272699...@qq.com>;"gromacs.org_gmx-users"<gromacs.org_gmx-users@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";<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
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