[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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