[gmx-users] Implicit solvent - Gromacs 4.5.4

[lina]

On Tue, Feb 28, 2012 at 10:07 PM, Steven Neumann <s.neumann08 at gmail.com> wrote:
> Thank you Vedat!
>
> Why do you use -DFLEXIBLE in md and in em?
> Why dont you use constraint algorithm (LINCS) in your simulation?

Otherwise, the system is easily explode with lots of LINCS warning.

Also thanks Vedat for sharing,

Best regards,

>
> 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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