[gmx-users] Implicit solvent - Gromacs 4.5.4

Steven Neumann s.neumann08 at gmail.com
Tue Feb 28 15:18:08 CET 2012


Thank you all!

How about -DFLEXIBLE in both em and md?

Steven

On Tue, Feb 28, 2012 at 2:13 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> lina wrote:
>
>> 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.
>>
>>
> A system that is unstable will cause the LINCS algorithm to fail, but
> turning off constraints does not prevent a system from becoming unstable or
> crashing.
>
> -Justin
>
>
> 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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>>>
>>>
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> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
>
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