[gmx-users] Pulling a CG protein
XAvier Periole
x.periole at rug.nl
Thu Jul 30 09:29:46 CEST 2009
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: johntus at berkeley.edu
>
>
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