[gmx-users] Implicit solvent - Gromacs 4.5.4
Justin A. Lemkul
jalemkul at vt.edu
Tue Feb 28 15:13:21 CET 2012
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
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