[gmx-users] Using TIP4P(2005) with GROMOS-53a6

[Catarina A. Carvalheda dos Santos]

Hi,

Smith is right. 53A6 was parametrized using the SPC water model:
http://onlinelibrary.wiley.com/doi/10.1002/jcc.20090/abstract.

Regards,

On 14 September 2015 at 14:44, Smith, Micholas D. <smithmd at ornl.gov> wrote:

> As far as I am aware, GROMOS53A6 does not play nice with water models
> other than SPC/E
>
> ===================
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Pallavi
> Banerjee <pallavisept at students.iiserpune.ac.in>
> Sent: Monday, September 14, 2015 9:43 AM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Using TIP4P(2005) with GROMOS-53a6
>
> Hello users,
>
> I am simulating a polymer in TIP4P(2005) water with GROMOS53a6 as the force
> field. I am using the same mdp options as has been provided in the source
> website. The following error shows up:
>
> " Molecule type 'SOL' has 6 constraints.
>   For stability and efficiency there should not be more constraints than
>   internal number of degrees of freedom: 3 "
>
> I tried a sample run with just the water, but the same happens. Could
> someone provide some valuable insight?
>
> Following are the mdp options:
>
> ; RUN CONTROL
> integrator               = md
> nsteps                   = 500000
> dt                       = 0.001
> ; NEIGHBOR SEARCHING
> cutoff-scheme            = Verlet
> nstlist                  = 1
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 0.85
> domain-decomposition     = no
> ; OUTPUT CONTROL
> nstxout                  = 10000
> nstvout                  = 10000
> nstxtcout                =10000
> nstlog                   =1000
> nstenergy                =1000
> ; OPTIONS FOR BONDS     =
> constraints              = all-angles
> ; Type of constraint algorithm =
> constraint-algorithm     = shake
> ; Do not constrain the start configuration =
> unconstrained-start      = no
> ; Relative tolerance of shake =
> shake-tol                = 1e-6
> ; 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
>
> ; OPTION FOR ELECTROSTATIC AND VDW
> coulombtype              = PME
> rcoulomb_switch          = 0
> rcoulomb                 = 0.85
> ; Dielectric constant (DC) for cut-off or DC of reaction field
> epsilon_rf                = 3.5
> ; Method for doing Van der Waals
> vdw-type                 = Cut-off
> ; cut-off lengths
> rvdw_switch              = 0
> rvdw                     = 0.85
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr                 = EnerPres
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension          = 1.0
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing           = 0.1
> ; 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
> ewald_geometry           = 3d
> ;epsilon_surface          = 0
> ;optimize_fft             = no
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> tcoupl                   =  V-rescale
> tc_grps                  =  System
> tau_t                    =  10
> ref_t                    =  300
> Pcoupl                   = no
> ;Pcoupltype               = isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau_p                    = 10
> compressibility          = 5.0e-5
> ref_p                    = 1.0
> gen_vel                  = yes
> gen_temp                 = 300
>
>
> Thanks and regards,
> Pallavi Banerjee.
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> The University of Dundee is a registered Scottish Charity, No: SC015096
>
> --
> Catarina A. Carvalheda
>
> PhD Student
> Computational Biology Division
> School of Life Sciences
> University of Dundee
> DD1 5EH, Dundee, Scotland, UK
>