[gmx-users] RE: Is non-linear data output/storage possible?
Neha
nshafique at wesleyan.edu
Tue Jul 2 19:23:02 CEST 2013
Hi,
So the commands are:
grompp -f 10step.mdp -p dppc_bilayer.top -o 10step.tpr -c dppc_bilayer.gro
mdrun -nt 4 -s 10step.tpr -c nonlinear.gro -e nonlinear.edr -x nonlinear.xtc
-o nonlinear.trr -g nonlinear.log -cpo nonlinear.cpt -rdd 2.5
grompp -f 100step.mdp -c 10step.tpr -p dppc_bilayer.top -o 100step.tpr -t
nonlinear.cpt
mdrun -nt 4 -s 100step.tpr -c nonlinear.gro -e nonlinear.edr -x
nonlinear.xtc -o nonlinear.trr -g nonlinear.log -cpi nonlinear.cpt -cpo
nonlinear.cpt -rdd 2.5
Up till this point the output is what I would expect. However now I try to
use the 10step mdp again in order to save it every ten time steps -
grompp -f 10step.mdp -c 100step.tpr -p dppc_bilayer.top -o 10step.tpr -t
nonlinear.cpt
mdrun -nt 4 -v -s 10step.tpr -c nonlinear.gro -e nonlinear.edr -x
nonlinear.xtc -o nonlinear.trr -g nonlinear.log -cpi nonlinear.cpt -cpo
nonlinear.cpt -rdd 2.5
And at this mdrun I get WARNING: This run will generate roughly
186617909559164928 Mb of data
starting mdrun 'DPPC BILAYER'
100 steps, infinite ps (continuing from step 1000, 20.0 ps).
This is the saving every 10 steps mdp file, the hundred step is identical
except steps is a 1000 and nstxout is 100.
; VARIOUS PREPROCESSING OPTIONS =
title = Martini
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 0.0
dt = 0.02
nsteps = 100
; number of steps for center of mass motion removal =
nstcomm = 1
comm-grps = DPPC W
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 10
nstvout = 10
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 100
nstenergy = 10
; Output frequency and precision for xtc file =
nstxtcout = 100
xtc_precision = 10
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps = DPPC W
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or none =
pbc = xyz
; nblist cut-off =
rlist = 1.2
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths =
rvdw_switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = Berendsen
; Groups to couple separately =
tc-grps = DPPC W
; Time constant (ps) and reference temperature (K) =
tau_t = 1.0 1.0
ref_t = 325 325
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 1.0 1.0
compressibility = 3e-5 3e-5
ref_p = 1.0 1.0
nstpcouple = 5
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
gen_temp = 325
gen_seed = 473529
; OPTIONS FOR BONDS =
constraints = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start = no
; Highest order in the expansion of the constraint coupling matrix
=lincs_order = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle = 30
--
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