[gmx-users] Implicit solvent - Gromacs 4.5.4
Steven Neumann
s.neumann08 at gmail.com
Tue Feb 28 17:56:38 CET 2012
I run energy minimization of my protein with implicit solvent:
> 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 = 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 = 2.25936
>
And I obtained:
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 30000
Step Time Lambda
0 0.00000 0.00000
Steepest Descents converged to Fmax < 1000 in 1 steps
Potential Energy = inf
Maximum force = 0.0000000e+00 on atom 0
Norm of force = nan
Can you please explain?
Steven
> On Tue, Feb 28, 2012 at 2:29 PM, Vedat Durmaz <durmaz at zib.de> wrote:
>
>> **
>> actually, as far as i know, the -DFLEXIBLE argument has no effect on
>> simulations without explicit water ?!
>>
>> i just copied the "define" line from my explicit simulation systems ..
>> so, the only define value, that has a meaning is -DPOSRESHELIX.
>>
>> i didn't use constraints for the first time in my life since implicit
>> solvent simulations incorporate a much smaller number of atoms and are
>> therefore not that expensive computationally. i always use this setting for
>> my explicit simulations only in order to increase the step size to 2fs with
>> a clear conscience ...
>>
>> best wishes
>> vedat
>>
>>
>> Am 28.02.2012 15:18, schrieb Steven Neumann:
>>
>> 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
>>>>>>>
>>>>>> --
>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>> Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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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
>>>
>>> ========================================
>>>
>>> --
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>>
>>
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>
>
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