[gmx-users] Pulling in GROMACS 4.0.3

[Johnny Lam]

Hi again,


I am trying to pull apart a CG protein (to verify CG results with those of
already published works using atomistic MD). Using the previous
suggestions, my new pull code is the following:

title                    = Martini
cpp                      = /usr/bin/cpp

integrator               = md
; start time and timestep in ps
tinit                    = 0.0
dt                       = 0.030
nsteps                   = 2500
; number of steps for center of mass motion removal =
nstcomm                  = 1
comm-grps		 =

; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout                  = 2500
nstvout                  = 2500
nstfout                  = 0
; Output frequency for energies to log file and energy file =
nstlog                   = 1000
nstenergy                = 1000
; Output frequency and precision for xtc file =
nstxtcout                = 33
xtc_precision            = 100
; 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               =

; 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                    = 1.4

; 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


; Temperature coupling   =
tcoupl                   = V-Rescale
; Groups to couple separately =
tc-grps                  = PROTEIN W
; Time constant (ps) and reference temperature (K) =
tau_t                    = 0.3 0.3
ref_t                    = 323 323
; Pressure coupling      =
Pcoupl                   = berendsen
Pcoupltype               = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p                    = 3.0
compressibility          = 3e-5
ref_p                    = 1.0

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel                  = no
gen_temp                 = 323
gen_seed                 = 666


constraints              = none
; Type of constraint algorithm =
constraint_algorithm     = SHAKE
; 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          = 60

; FREEZE GROUP
; freezegrps = freeze
; freezedim  = Y Y Y

; Pulling

pull                =  umbrella

pull_geometry       =  distance

pull_start          =  yes

pull_nstxout        =  10

pull_nstfout        =  10

pull_ngroups        =  1

pull_group0         =  freeze

pull_group1         =  pull

pull_init1          =  0.0 0.0 0.0

pull_rate1          =  5000.0

pull_k1             =  100


The reason why the number of time steps is quite small, the pull_rate
quite high, and the force constant low is because I wanted to verify that
the code actually works before doing the actual production run (around 13
ns). The issue I'm running into is that when I check the results using
VMD, it seems almost as if the simulation ignored all of my pull commands.
I changed the rate, force constant, and the # timesteps to many different
values but to no avail. Every result seems to indicate that my pull
commands were not read (nothing happens aside from vibration). I highly
doubt that there is a bug (as mentioned in an earlier post). I don't know
why this is happening. Is there something wrong with the code? I really
appreciate the help!


--Johnny


-------------------------------------------------
Johnny Lam
ISPE Berkeley Chapter External Vice President
Department of Bioengineering
College of Engineering
University of California, Berkeley
Tel: (408) 655- 6829
Email: johntus at berkeley.edu