[gmx-users] Implicit solvent - Gromacs 4.5.4
Steven Neumann
s.neumann08 at gmail.com
Tue Feb 28 22:12:38 CET 2012
Thank you Vedat!!!
On Tue, Feb 28, 2012 at 8:35 PM, vedat durmaz <durmaz at zib.de> wrote:
> **
>
> 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> 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
>>>>>>>>
>>>>>>> --
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>>>>>>
>>>>>>
>>>>>> --
>>>>>> gmx-users mailing list gmx-users at gromacs.org
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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 <%28540%29%20231-9080>
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>> ========================================
>>>>
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>>
>>
>
>
>
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