[gmx-users] constraining multiple types of bonds
tarak karmakar
tarak20489 at gmail.com
Thu Nov 8 19:07:19 CET 2012
Dear All,
In my system I need to fix three types of bonds
1) Metal-Ligand distance at a particular value given in PDB ( not covalent)
2) I need to fix some of the bond lengths (covalent) for the substrate molecule.
3) Lastly the covalent H-bonds ( C-H, N-H, O-H etc.)
My input .mdp file is given below
; 7.3.3 Run Control
integrator = md-vv ; md integrator
tinit = 0 ; [ps] starting time for run
dt = 0.001 ; [ps] time step for integration
nsteps = 5000000 ; maximum number of
steps to integrate, 0.001 * 20,00,000 = 2 ns
nstcomm = 1 ; [steps] frequency of
mass motion removal
comm_grps = Protein Non-Protein ; group(s) for center
of mass motion removal
; 7.3.8 Output Control
nstxout = 5000 ; [steps] freq to write
coordinates to trajectory
nstvout = 5000 ; [steps] freq to write
velocities to trajectory
nstfout = 5000 ; [steps] freq to write
forces to trajectory
nstlog = 1000 ; [steps] freq to write
energies to log file
nstenergy = 1000 ; [steps] freq to write
energies to energy file
nstxtcout = 1000 ; [steps] freq to write
coordinates to xtc trajectory
xtc_precision = 1000 ; [real] precision to
write xtc trajectory
xtc_grps = System ; group(s) to write to
xtc trajectory
energygrps = System ; group(s) to write to
energy file
; 7.3.9 Neighbor Searching
nstlist = 1 ; [steps] freq to
update neighbor list
ns_type = grid ; method of updating
neighbor list
pbc = xyz ; periodic boundary
conditions in all directions
rlist = 1.2 ; [nm] cut-off
distance for the short-range neighbor list
nsttcouple = 1
nstpcouple = 1
; 7.3.10 Electrostatics
coulombtype = PME ; Particle-Mesh Ewald
electrostatics
rcoulomb = 1.2 ; [nm] distance for
Coulomb cut-off
; 7.3.11 VdW
vdwtype = cut-off ; twin-range cut-off
with rlist where rvdw >= rlist
rvdw = 1.2 ; [nm] distance for LJ cut-off
DispCorr = EnerPres ; apply long range
dispersion corrections for energy
; 7.3.13 Ewald
fourierspacing = 0.12 ; [nm] grid spacing
for FFT grid when using PME
pme_order = 4 ; interpolation order
for PME, 4 = cubic
ewald_rtol = 1e-5 ; relative strength of
Ewald-shifted potential at rcoulomb
; 7.3.14 Temperature Coupling
tcoupl = Nose-Hoover ; Nose-Hoover
temperature coupling
tc_grps = Protein Non-Protein ; groups to
couple seperately to temperature bath
tau_t = 1.0 1.0 ; [ps] time
constant for coupling
ref_t = 300 300 ; [K]
reference temperature for coupling
; 7.3.15 Pressure Coupling
pcoupl = MTTK ; pressure
coupling where box vectors are variable
pcoupltype = isotropic ; pressure
coupling in x-y-z directions
tau_p = 1.0 ; [ps] time
constant for coupling
compressibility = 4.5e-5 ; [bar^-1]
compressibility
ref_p = 1.0 ; [bar]
reference pressure for coupling
; 7.3.17 Velocity Generation
gen_vel = no ; velocity
generation turned off
; 7.3.18 Bonds
constraints = h-bonds
constraint_algorithm = SHAKE ; SHAKE
Constraint Solver
shake_tol = 1.0e-5
So I'm bit confused how to implement constraints algorithm for these
type of problem. If I do use the above set up then it is showing
following error
Program mdrun, VERSION 4.5.5
Source code file: invblock.c, line: 79
Fatal error:
Double entries in block structure. Item 5247 is in blocks 1371 and 1370
Cannot make an unambiguous inverse block.
Thanks
--
Tarak
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