[gmx-users] Implicit solvent - Gromacs 4.5.4
Vedat Durmaz
durmaz at zib.de
Tue Feb 28 15:29:32 CET 2012
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
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> lina wrote:
>
> On Tue, Feb 28, 2012 at 10:07 PM, Steven Neumann
> <s.neumann08 at gmail.com <mailto: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 <mailto: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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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
> <tel:%28540%29%20231-9080>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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