[gmx-users] nvt problem

[Mark Abraham]

Hi,

You've got too many sources of possible complications. Simplify. Does gold
in water work? With and without freeze groups? Does peptide in water work?
Why aren't you generating velocities at the right temperature for the start
of your NVT?

Mark

On Sat, Nov 8, 2014 at 6:10 AM, Lovika Moudgil <lovikamoudgil at gmail.com>
wrote:

> Hi Everyone ,
>
> I am having a problem in NVT of system . In my system I have Gold and
> aminoacid . For Gold I am using GolP forcefield and for aminoacid using
> OPLSAA forcefield . I have done energy minimization of my system but when I
> am doing NVT I am getting error of water is not getting settled . I am
> confused How it got minimize if water is not settled in system .I have
> tried changing parameters of NVT.mdp file but noting worked . Can any body
> help me what can be the root cause for this . I will be thankful for
> guidance .
>
> My NVT.mdp
> ; 7.3.2 Preprocessing
> define                  = -DPOSRES      ; defines to pass to the
> preprocessor
>
> ; 7.3.3 Run Control
> integrator              = md                    ; md integrator
> tinit                   = 0                     ; [ps] starting time for
> run
> dt                      = 0.001                 ; [ps] time step for
> integration
> nsteps                  = 25000                 ; maximum number of steps
> to integrate, 0.001 * 25,000 = 25 ps
> 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                 = 25000         ; [steps] freq to write coordinates
> to trajectory
> nstvout                 = 25000         ; [steps] freq to write velocities
> to trajectory
> nstfout                 = 25000         ; [steps] freq to write forces to
> trajectory
> nstlog                  = 50           ; [steps] freq to write energies to
> log file
> nstenergy               = 100           ; [steps] freq to write energies to
> energy file
> nstxtcout               = 100           ; [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                   = 1.4           ; [nm] cut-off distance for the
> short-range neighbor list
>
> ; 7.3.10 Electrostatics
> coulombtype             = PME           ; Particle-Mesh Ewald
> electrostatics
> rcoulomb                = 1.4           ; [nm] distance for Coulomb cut-off
>
> ; 7.3.11 VdW
> vdwtype                 = cut-off       ; twin-range cut-off with rlist
> where rvdw >= rlist
> rvdw                    = 1.4           ; [nm] distance for LJ cut-off
> DispCorr                = EnerPres      ; apply long range dispersion
> corrections
>
> ; 7.3.13 Ewald
> fourierspacing          = 0.10          ; [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                     ; temperature
> coupling with Berendsen-thermostat
> tc_grps                 = Protein    Non-Protein        ; groups to couple
> seperately to temperature bath
> tau_t                   = 0.1        0.1                ; [ps] time
> constant for coupling
> ref_t                   = 310        310                ; [K] reference
> temperature for coupling
>
> ; 7.3.17 Velocity Generation
> gen_vel                 = no           ; generate velocities according to
> Maxwell distribution of temperature
> gen_temp                = 310           ; [K] temperature for Maxwell
> distribution
> gen_seed                = -1            ; [integer] used to initialize
> random generator for random velocities
>
> ; 7.3.18 Bonds
> constraints             = all-bonds     ; convert all bonds to constraints
> constraint_algorithm    = LINCS         ; LINear Constraint Solver
> lincs_order             = 4             ; highest order in the expansion of
> the contraint coupling matrix
> lincs_iter              = 1             ; number of iterations to correct
> for rotational lengthening
> lincs_warnangle         = 80            ; [degrees] maximum angle that a
> bond can rotate before LINCS will complain
> ; To keep au surface in place, freeze Au atoms.
> ; The AU group has been defined via make_ndx
> ; to contains all the AU atoms ('a AU').
> freezegrps               = AU  AUI
> freezedim                = Y Y Y Y Y Y
> comm_mode                 = none
>
>
>
> Regards
> Lovika
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