Oh ! I'm sorry Justin Actually 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. Thanks On Wed, Nov 7, 2012 at 11:54 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/7/12 10:46 AM, tarak karmakar wrote: >> >> Dear All, >> >> As I am facing the following problem while using SHAKE to constrain >> some bonds, I have checked the mailing list but I think, this issue >> has not been resolved. So if anyone knows the solution kindly inform >> me. >> >> 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. >> >> >> Actually I need to fix some of the ligand bonds along with the >> covalent h-bonds (C-H, N-H, O-H etc.). >> What do you suggest to use for this multiple constraining problem ? >> Should I use SHAKE/LINCS for both type of bonds or anything else ? >> > > Can you explain in a bit greater depth what you're trying to do? Are you > trying to constrain distances between atoms that are not covalently bonded? > In that case, restraints are likely more appropriate than constraints, but > we'll need more detail before anyone can give you any really productive > suggestions. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tarak -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
