Вы находитесь на странице: 1из 7

Distance restraint Gromacs http://www.gromacs.org/Documentation/How-tos/Distance_Restraints http://gromacs.5086.n6.nabble.com/Generation-of-the-Distance-Restraints-td4570246i20.

html
The force is the negative of the derivative of the potential with respect to the distance. So the force is also zero between r_0 and r_1. So if you want a distance to be restrained between 1 and 2 nm, set r_0=1 and r_1=2. That way the force is zero if the distance is satisfactory, and non-zero when it is not.

opciones mdp http://manual.gromacs.org/current/online/mdp_opt.html mailing list: distance restraint ejemplo mdp


title cpp include define integrator dt nsteps nstxout nstvout nstlog nstenergy nstxtcout xtc_grps energygrps nstlist ns_type rlist coulombtype rcoulomb rvdw tcoupl tc-grps tau_t ref_t Pcoupl tau_p compressibility ref_p gen_vel gen_temp gen_seed constraints = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = Yo /lib/cpp -I../top md 0.002 500000 5000 5000 5000 250 250 Protein Protein SOL 10 grid 0.8 cut-off 1.4 0.8 Berendsen Protein SOL 0.1 0.1 300 300 Berendsen 1.0 4.5e-5 1.0 yes 300 173529 all-bonds

With this input grompp will produce an mdout.mdp with all the options and descriptions:
; VARIOUS PREPROCESSING OPTIONS = title = Yo cpp = /lib/cpp include = -I../top define = ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit = 0 dt = 0.002 nsteps = 500000 ; number of steps for center of mass motion removal = nstcomm = 1 comm-grps = ; LANGEVIN DYNAMICS OPTIONS = ; Temperature, friction coefficient (amu/ps) and random seed = bd-temp = 300 bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS = ; Force tolerance and initial step-size = emtol = 100 emstep = 0.01 ; Max number of iterations in relax_shells = niter = 20 ; Frequency of steepest descents steps when doing CG = nstcgsteep = 1000 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 5000 nstvout = 5000 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 5000 nstenergy = 250 ; Output frequency and precision for xtc file = nstxtcout = 250 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc_grps = Protein ; Selection of energy groups = energygrps = Protein SOL ; 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 = 0.8 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = cut-off rcoulomb-switch = 0 rcoulomb = 1.4 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r = 1 ; Method for doing Van der Waals = vdw-type = Cut-off ; cut-off lengths = rvdw-switch = 0 rvdw = 0.8 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order = 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = Berendsen ; Groups to couple separately = tc-grps = Protein SOL ; Time constant (ps) and reference temperature (K) = tau_t = 0.1 0.1 ref_t = 300 300 ; Pressure coupling = Pcoupl = Berendsen Pcoupltype = Isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; SIMULATED ANNEALING CONTROL = annealing = no ; Time at which temperature should be zero (ps) = zero-temp_time = 0 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 300

gen_seed

= 173529

; OPTIONS FOR BONDS = constraints = all-bonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol = 0.0001 ; 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 ; Convert harmonic bonds to morse potentials = morse = no ; NMR refinement stuff = ; Distance restraints type: No, Simple or Ensemble = disre = No ; Force weighting of pairs in one distance restraint: Equal or Conservative = disre-weighting = Equal ; Use sqrt of the time averaged times the instantaneous violation = disre-mixed = no disre-fc = 1000 disre-tau = 0 ; Output frequency for pair distances to energy file = nstdisreout = 100 ; Free energy control stuff = free-energy = no init-lambda = 0 delta-lambda = 0 sc-alpha = 0 sc-sigma = 0.3 ; Non-equilibrium MD stuff = acc-grps = accelerate = freezegrps = freezedim = cos-acceleration = 0 energygrp_excl = ; Electric fields = ; Format is number of terms (int) and for all terms an amplitude (real) = ; and a phase angle (real) = E-x = E-xt = E-y = E-yt = E-z = E-zt = ; User defined thingies =

user1-grps user2-grps userint1 userint2 userint3 userint4 userreal1 userreal2 userreal3 userreal4

= = = = = = = = = =

0 0 0 0 0 0 0 0

http://gromacs.5086.n6.nabble.com/Distance-Restraints-on-Protein-possible-at-alltd4493374.html
4) prepare .tpr file grompp -f NPT_disres.mdp -c posre_NPT_rep1.gro -n index.ndx -p merged.top -t posre_NPT_rep1.cpt -o disre.tpr

5) mdrun mdrun-mpi -v -s disre.tpr -deffnm disre -pd

En foro
Dear gmx's user, May I asked you some technicl Questions? Do you know how to make distance restraint in gromacs? what I did I have created file name "disre.itp" as shown below [ distance_restraints ] ; ai aj type index type low up1 up2 fac 489 1133 1 1 1 0.25 0.35 0.40 1.0 489 1164 1 2 1 0.25 0.35 0.40 1.0 490 1127 1 3 1 0.25 0.35 0.40 1.0 490 1167 1 4 1 0.25 0.35 0.40 1.0 in md.mdp file: title cpp constraints define integrator dt nsteps nstcomm nstxout nstvout nstfout nstlog = M2_amand in POPC = /lib/cpp = all-bonds = -DDISRES = md = 0.002 ; ps ! = 500000 ; total 1000 ps = 1 ns ! = 1 = 250 = 1000 = 0 = 100

nstenergy = 100 nstlist = 10 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 pbc = xyz ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein POPC SOL Cl tau_t = 0.1 0.1 0.1 0.1 ref_t = 310 310 310 310 ; Energy monitoring energygrps = Protein POPC SOL Cl ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp = 310.0 disres = simple in topology.top file I added... ; Include distance restraint file #ifdef DISRES #include "disre.itp" #endif

http://comments.gmane.org/gmane.science.biology.gromacs.user/15907 I need to use simple distance restraints of 12.5 A between two CA atoms of two residues. I am using the following lines in the .itp file #ifdef DDISRES [distance_restraints] ;ai aj type index type' low up1 up2 fac 1703 1712 1 0 1 11.5 12.0 12.5 1.0 The first feww line of .mdp file for minimisation of protein alone is ; Preprocessing ;

title cpp define

= ${MOL} = /lib/cpp ;Preprocessor = -DDISRES ;For cg, and also steep

http://comments.gmane.org/gmane.science.biology.gromacs.user/51387 There are a few possibilities.

1. Numbering in [distance_restraints] is not based on .gro numbering. The atom numbers supplied are only relevant within the [moleculetype] to which they belong, much like [position_restraints]. Also make sure that the [distance_restraints] block is in the correct location in the topology.

2. You've omitted the dihre_fc keyword, though it is set to 1000 by default. Check the mdout.mdp file or your .tpr file to ensure that you have a sensible value here. Setting values of fac that high are unnecessary.