[gmx-users] Pulling a CG protein

[Johnny Lam]

Dear gromacs users,

Hi, I am trying to pull apart a relatively large protein (CG using the
martini force field) by pulling on two groups in opposite directions. To
do this, I will be using the following .mdp file. However, I am almost
certain that it contains errors:

title                    = Martini
cpp                      = /usr/bin/cpp

; RUN CONTROL PARAMETERS =
; MARTINI - Most simulations are stable with dt=40 fs,
; some (especially rings) require 20-30 fs.
; The range of time steps used for parametrization
; is 20-40 fs, using smaller time steps is therefore not recommended.

integrator               = md
; start time and timestep in ps
tinit                    = 0.0
dt                       = 0.030
nsteps                   = 17000
; 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                = 1000
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               =

; NEIGHBORSEARCHING PARAMETERS =
; MARTINI - no need for more frequent updates
; or larger neighborlist cut-off due
; to the use of shifted potential energy functions.

; 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

; OPTIONS FOR ELECTROSTATICS AND VDW =
; MARTINI - vdw and electrostatic interactions are used
; in their shifted forms. Changing to other types of
; electrostatics will affect the general performance of
; the model.

; 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 =
; MARTINI - normal temperature and pressure coupling schemes
; can be used. It is recommended to couple individual groups
; in your system seperately.

; 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

; OPTIONS FOR BONDS     =
; MARTINI - for ring systems constraints are defined
; which are best handled using Lincs.

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          = 60

; FREEZE GROUP

; Pulling
pull                =  afm
pull_geometry       =  direction
pull_start          =  no
pull_nstxout        =  10
pull_nstfout        =  10
pull_ngroups        =  2
pull_group0         =
pull_group1         =  pull
pull_vec1           =  -0.1764 -0.9823 -0.0625
pull_init1          =  -0.1764 -0.9823 -0.0625
pull_rate1          =  0.0001
pull_k1             =  1000
pull_group2         =  freeze
pull_vec2           =  0.1764 0.9823 0.0625
pull_init2          =  0.1764 0.9823 0.0625
pull_rate2          =  0.0000000001
pull_k2             =  5000


The reason why group 2 has such a high force constant and low pull rate is
because I wanted to simulate putting a harmonic constraint on the freeze
group. However, when I process this .mdp with grompp, I get the following
message:

WARNING 1 [file md_vinculin.mdp, line unknown]:
  Unknown or double left-hand 'pull_group2' in parameter file



WARNING 2 [file md_vinculin.mdp, line unknown]:
  Unknown or double left-hand 'pull_vec2' in parameter file


The version of gromacs I have running on my powerpc is 4.0.5 so the pull
code should be implemented in the .mdp file. I am not sure if I specified
the parameters correctly. Please help! Thanks!

--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