[gmx-users] constraining multiple types of bonds
tarak karmakar
tarak20489 at gmail.com
Fri Nov 9 05:36:17 CET 2012
Thanks Justin
As you see in the .mdp file I have used SHAKE. So if I want to fix
some C-C or C-O then what algorithm I have to use ?
In my topology file I have specified following bonds to be
constrained. The first two are covalent and the last one is M-L
non-covalent bond.
[ constraints ]
; index1 index2 funct length(nm)
6062 6063 1 0.11490000000
6062 6064 1 0.11490000000
6060 4309 1 0.21000000000
Now while implementing SHAKE it is showing
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.
Please suggest me the exact protocol.
Thanks
On Fri, Nov 9, 2012 at 2:18 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 11/8/12 1:07 PM, tarak karmakar wrote:
>>
>> 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)
>
>
> These require a merged [moleculetype] and are best implemented using simple
> harmonic interactions (bond type 6) or distance restraints.
>
>
>> 2) I need to fix some of the bond lengths (covalent) for the substrate
>> molecule.
>
>
> Some, but not all? That doesn't make sense to me.
>
>
>> 3) Lastly the covalent H-bonds ( C-H, N-H, O-H etc.)
>>
>
> These are created using the .mdp settings shown below.
>
> -Justin
>
>
>>
>> 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
>>
>
> --
> ========================================
>
> 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
>
> ========================================
> --
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--
Tarak
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