[gmx-users] Implicit solvent tutorial

[lina]

On Thu, Dec 8, 2011 at 11:26 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> lina wrote:
>>
>> On Thu, Dec 8, 2011 at 9:50 PM, Gianluca Santoni
>> <gianluca.santoni at ibs.fr> wrote:
>>>
>>> Hi gmx_users,
>>> is there any tutorial for implicit solvent simulation available?
>>
>>
>> Hi,
>>
>> I tried it few days ago.
>>
>> 1] pdb2gmx the water model choose none.
>>
>> 2] after editconf, go to energy minimization directly
>> * It's important to relax the system well.
>>
>> 3] NVT
>>
>> 4] You may find one .mdp file from gromacs-gpubench-dhfr.tar.gz
>> At bottom also attached the one I tried.
>>
>> If some part is wrong, please let me know.
>>
>
> You should not use PBC. Cutoffs should be infinite (i.e. all set to zero).
Thanks, I noticed the example in the gromacs-gpubench-dhfr.tar.gz use
PBC=no and Cut-off is infinite.

>  I have never achieved stable simulations with finite cutoffs, even long
> ones, in implicit solvent simulations.

Thanks for reminding.

>
> The tcoupl setting is ignored when using the sd integrator, and there is
> very little need to do any position restraining in implicit solvent
> simulations, as there is no solvent to relax, you're just restraining the
> protein and not accomplishing anything.  gen_vel should be set to "yes" to
> generate velocities following EM.

Thanks again, I restrained some peptides, another peptides are free.
hopefully it will work.

>
> -Justin
>
>
>> Thanks,
>>
>> define          = -DPOSRES
>> integrator      = sd
>> nsteps          = 1000000000
>> dt              = 0.0005
>> nstxout         = 1000
>> nstvout         = 1000
>> nstxtcout       = 1000
>> nstenergy       = 1000
>> nstlog          = 1000
>> continuation    = yes
>> constraints     = all-bonds
>> ns_type         = grid
>> nstlist         = 1.0
>> rlist           = 1.0
>> rcoulomb        = 1.0
>> rvdw            = 1.0
>> coulombtype     = Cut-off
>> pme_order       = 4
>> fourierspacing  = 0.16
>> tcoupl          = V-rescale
>> tc-grps         = A B C
>> tau_t           = 0.1 0.1 0.1
>> ref_t           = 300 300 300
>> pbc             = xyz
>> gen_vel         = no
>> ld_seed         = -1
>> implicit_solvent = GBSA
>> gb_algorithm     = OBC
>> nstgbradii       = 1.0
>> rgbradii         = 1.0
>> gb_epsilon_solvent = 80
>> gb_dielectric_offset = 0.009
>> sa_algorithm         = Ace-approximation
>> sa_surface_tension   = 0.0054
>>
>>
>>> Thanks!
>>>
>>> --
>>> Gianluca Santoni,
>>> Institut de Biologie Structurale
>>> 41 rue Horowitz
>>> Grenoble
>>> _________________________________________________________
>>> Please avoid sending me Word or PowerPoint attachments.
>>> See http://www.gnu.org/philosophy/no-word-attachments.html
>>>
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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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