Hi Johnny,
I am not familiar with pulling and even less with gromacs but I would be
very cautious in using the MARTINI force field for the kind of
simulation
you are doing.
This CG model has not been tested at all for this and it might not be
very good at it! But I would be very interested in knowing how it
actually
perform.
XAvier.
On Jul 30, 2009, at 1:04 AM, Johnny Lam wrote:
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: john...@berkeley.edu
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