[gmx-users] Implicit solvent - Gromacs 4.5.4

[Steven Neumann]

Thank you Vedat!

Why do you use -DFLEXIBLE in md and in em?
Why dont you use constraint algorithm (LINCS) in your simulation?

Steven

On Tue, Feb 28, 2012 at 12:14 PM, Vedat Durmaz <durmaz at zib.de> wrote:

>
> hi steven,
>
> i've been simulating a 33 AA peptide for the past two days using implicent
> solvent in order to achieve a proper folding.
>
> i haven't added counterions, however, the systems shows nice results
> according to what i've expected. the mdrun command (for the extension) for
> our hardware looks as follows:
>
> mpiexec -np 4 mdrun -pd -s md.tpr -append -cpi md.cpt -deffnm md 2>&1
>
> and here's the mdp file for the energy minimization:
>
> define              =  -DFLEXIBLE
> constraints         =  none
> integrator          =  steep
> dt                  =  0.001    ; ps
> nsteps              =  30000
> vdwtype             =  cut-off
> coulombtype         =  cut-off
> pbc                 =  no
> nstlist             =  0
> ns_type             =  simple
> rlist               =  0       ; this means all-vs-all (no cut-off), which
> gets expensive for bigger systems
> rcoulomb            =  0
> rvdw                =  0
> comm-mode           =  angular
> comm-grps           =  Protein
> optimize_fft        =  yes
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  5.0
> emstep              =  0.01
> ;
> ; Implicit solvent
> ;
> implicit_solvent    =  GBSA
> gb_algorithm        =  Still ; HCT ; OBC
> nstgbradii          =  1
> rgbradii            =  0   ; [nm] Cut-off for the calculation of the Born
> radii. Currently must be equal to rlist
> gb_epsilon_solvent  =  80    ; Dielectric constant for the implicit solvent
> ; gb_saltconc       =  0     ; Salt concentration for implicit solvent
> models, currently not used
> sa_algorithm        =  Ace-approximation
> sa_surface_tension  = -1
>
>
> and for the md run:
>
> define              =  -DPOSRESHELIX ; -DFLEXIBLE -DPOSRES
> constraints         =  none
> integrator          =  md
> dt                  =  0.001   ; ps
> nsteps              =  1000000000 ; 100000 ps = 100 ns
> nstcomm             =  10
> nstcalcenergy       =  10
> nstxout             =  1000     ; frequency to write coordinates to output
> trajectory
> nstvout             =  0       ; frequency to write velocities to output
> trajectory; the last velocities are always written
> nstfout             =  0       ; frequency to write forces to output
> trajectory
> nstlog              =  1000         ; frequency to write energies to log
> file
> nstenergy           =  1000     ; frequency to write energies to edr file
>
> vdwtype             =  cut-off
> coulombtype         =  cut-off
>
> pbc                 =  no
>
> nstlist             =  0
> ns_type             =  simple
> rlist               =  0       ; this means all-vs-all (no cut-off), which
> gets expensive for bigger systems
> rcoulomb            =  0
> rvdw                =  0
>
> comm-mode           =  angular
> comm-grps           =  system
>
> optimize_fft        =  yes
>
> ; V-rescale temperature coupling is on
> Tcoupl              =  v-rescale
> tau_t               =  0.1
> tc_grps             =  system
> ref_t               =  300
> ; Pressure coupling is off
> Pcoupl              =  no
> ; Generate velocites is on
> gen_vel             =  yes
> gen_temp            =  300
> gen_seed            =  -1
>
> ;
> ; Implicit solvent
> ;
> implicit_solvent    =  GBSA
> gb_algorithm        =  Still ; HCT ; OBC
> nstgbradii          =  1
> rgbradii            =  0   ; [nm] Cut-off for the calculation of the Born
> radii. Currently must be equal to rlist
> gb_epsilon_solvent  =  80    ; Dielectric constant for the implicit solvent
> ; gb_saltconc       =  0     ; Salt concentration for implicit solvent
> models, currently not used
> sa_algorithm        =  Ace-approximation
> sa_surface_tension  = -1
>
>
> best regards,
> vedat
>
>
> Am 28.02.2012 11:59, schrieb Steven Neumann:
>
> Dear Gmx Users,
>> I am using Gromacs 4.5.4 and I would like to implement implicit solvent
>> for folding of my protein. I read mailing list and it is still confusing
>> for me.
>> Is it proper to use counterions within the system? If not, how can I
>> obtain netral system?
>> Do we use cut off for vdw and coulombic interactions?
>> What kind of integrator should be used with a timestep?
>> I will appreciate an mdp file for protein folding! Thank you
>> Steven
>>
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