[gmx-users] Implicit solvent - Gromacs 4.5.4
vedat durmaz
durmaz at zib.de
Tue Feb 28 21:35:57 CET 2012
hi jan/steven (?),
you should know, in contrast to let's say justin lemkul, i haven't that
much experience with molecular simulations!
actually, i don't expect large differences in conformational/statistical
properties depending on the usage of lincs constraints. usually i use
them when simulating target ligand systems with explicit solvent in
order to save time. for these large systems (in the order of 100,000
atoms), i set emtol to about 300.
however, for this small peptide (33AA) i refrained from constraints and
set emtol to 5 which is achieved quite quickly. for a large protein with
implicit solvent i would probably set emtol to 50 or something like that.
according to your strange results:
i remember, i didn't do the energy minimization of the small peptide on
our computing cluster but on my local machine (six cpu-cores) with
gromacs-4.5.5 (no mpich, but openmpi). besides, i parameterized my
peptide using acpype (amber99sb force field) and didn't use editconf
(didn't set any box)! i just grompped the system and did the mdrun like
grompp -f ../em.mdp -c ../peptide.pdb -p ../peptide.top -o em.tpr
mdrun -v -deffnm em
and that's all .. 4 cores were used by mdrun.
hope, that helps
vedat
Am 28.02.2012 17:56, schrieb Steven Neumann:
> 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
> <mailto: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 <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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>
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