[gmx-users] RE: Is non-linear data output/storage possible?

[Neha]

Hi everybody,

I started changing init-step. Now I seem to have another problem. When I go
to switch to another 'block' it tells me that my input and checkpoint states
are not identical when I use mdrun the second time. I am not sure how they
can be any different as I only have one .cpt file in the directory.

My list of commands is right here - 

grompp -f 1step.mdp -c 315monolayer.gro -p dppc_monolayer.top -o
315monolayer.tpr

mdrun -nt 4 -s 315monolayer.tpr -c 315monolayer.gro -e 315monolayer.edr -o
315monolayer.trr -x 315monolayer.xtc -g 315monolayer.log -cpo
315monolayer.cpt -rdd 2.5

grompp -f 10step.mdp -c 315monolayer.tpr -p dppc_monolayer.top -o
315monolayer.tpr -t 315monolayer.cpt

mdrun -nt 4 -s 315monolayer.tpr -c 315monolayer.gro -e 315monolayer.edr -o
315monolayer.trr -x 315monolayer.xtc -g 315monolayer.log -cpi
315monolayer.cpt -cpo 315monolayer.cpt -rdd 2.5


Is there something I am doing wrong with continuing this simulation? 



This is the saving each step copy of the mdp file:
; 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                   = 10
init-step = 0
; 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                  = 1
nstvout                  = 1
nstfout                  = 0
; Output frequency for energies to log file and energy file =
nstlog                   = 5
nstenergy                = 10
; Output frequency and precision for xtc file =
nstxtcout                = 10
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                    = 310 310
; 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 0.0
ref_p                    = 0.0  0.0
nstpcouple               = 5

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel                  = no
gen_temp                 = 315
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

The 10step.mdp file is identical except it runs for 90 steps, init-step is
10 and nstxout is 10. 

I am guessing that this might have something to do with the frequency of
writing .cpt files? Otherwise I have no idea why this could be happening. 





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