Fwd: Re: [gmx-users] Constraints only on Backbone

[Justin A. Lemkul]

----- Forwarded message from "Justin A. Lemkul" <jalemkul at vt.edu> -----
    Date: Thu, 29 May 2008 09:08:47 -0400
    From: "Justin A. Lemkul" <jalemkul at vt.edu>
Reply-To: "Justin A. Lemkul" <jalemkul at vt.edu>
 Subject: Re: [gmx-users] Constraints only on Backbone
      To: bjoern.olausson at biochemtech.uni-halle.de

Quoting Bjoern Olausson <bjoern.olausson at biochemtech.uni-halle.de>:

> On Thursday 29 May 2008 13:39:58 you wrote:
> > Quoting Bjoern Olausson <bjoern.olausson at biochemtech.uni-halle.de>:
> > > Hi all,
> > >
> > > first of all, I am new to gromacs ... (trying to switch from amber to
> > > gromacs)
> > > as you can see from the following qestion:
> > >
> > > Is  there a way to apply constraints only to the backbone of my Proteine
> > > and let the sidechains "shake" (LINCS)
> >
> > Do you mean constraints or restraints?  These are different ideas in
> > Gromacs. Using LINCS or SHAKE would mean applying constraints to your
> > sidechains, so I don't understand the question.
> >
> Okay, I understand.
> So to make my ideas clear:
>
> I want to keep the backbone fixed and let the sidechains do whatever they
> want
> to do ( or actually use lincs) ;-)

So you'll want to *restrain* atomic positions and *constrain* bond lengths.

>
> this is my amber in file which I use after equilibration:
>  Running MD with fixed backbone
>  &cntrl
>   imin   = 0,
>   irest  = 1,
>   ntx    = 7,
>   ntb    = 2,
>   pres0  = 1.0,
>   ntp    = 1,
>   taup   = 2.0,
>   cut    = 10,
>   ntr    = 1,
>   ntc    = 1,
>   ntf    = 1,
>   tempi  = 300.0,
>   temp0  = 300.0,
>   ntt    = 3,
>   gamma_ln = 1.0,
>   nstlim = 2000000,
>   dt     = 0.001,
>   ntpr   = 500,
>   ntwx   = 4000,
>   ntwr   = 1000
>  /
> Keep Mainchain fixed
> 500.0
> FIND
> * * M *
> SEARCH
> RES 1 761
> END
> END
>
> and this is the current gromacs mdp file.
>
> title               =  bis ; Regular (non pr MD)
> cpp                 =  /usr/bin/cpp
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.002    ; ps !
> nsteps              =  1000000     ; total 2000.0 ps.
> nstcomm             =  1
> nstxout             =  500 ; collect data every 1.0 ps
> nstvout             =  0
> nstfout             =  0
> nstlist             =  10
> ns_type             =  grid
> rlist               =  0.9
> coulombtype         =  PME
> rcoulomb            =  0.9
> rvdw                =  0.9
> fourierspacing      =  0.12
> fourier_nx          =  0
> fourier_ny          =  0
> fourier_nz          =  0
> pme_order           =  4
> ewald_rtol          =  1e-5
> optimize_fft        =  yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  berendsen
> tau_t               =  0.1              0.1          0.1
> tc-grps             =  protein          sol          NA+
> ref_t               =  300              300          300

Never couple solvent and ions separately.  You're asking for an explosion.  See
here:

http://wiki.gromacs.org/index.php/Thermostats

> ; Pressure coupling on
> Pcoupl              =  berendsen
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
>
>
> > constraints         =  all-bonds
> This tells gromacs to shake all bonds with lincs, does it?

Your bonds will be *constrained* with LINCS if you specify

constraint_algorithm = lincs

>
> > define              =  -DPOSRES
> If I add the above, all atoms listed in the  itp file will be kept fixed, do
> they?

According to whatever is in your posre.itp file, yes.

>
> So if I want to keep all backbone atoms fixed, I have to generate a
> posres-backbone.itb file. Add the following to my protein.itb
> #ifdef POSRES
> #include "posres-backbone.itb"
> #endif
> So now every Atom  listed in the posres-backbone.itb is kept fixed.

Correct.  Note that the file format is .itp, not .itb.

>
> > If you want to apply constraints to the backbone atoms only, you can define
> > them explicitly in your topology and set 'constraints = none' in your .mdp
> > file.
> > If you want to apply restraints to the backbone atoms only, you can create
> > a posre.itp file from genpr.
>
> Just to get it right:
> constraints  == LINCS/SHAKE
> restraints == Put some force on Atoms to keep them in position.

Correct.

>
> By the way, is there a way to define the strength of the force whith which
> the
> Atoms are kept in place (like in the amber in file 500.0 kcal mol-1
> angstrom-2)

When creating the topology file using pdb2gmx, use the -posrefc option.  Note
that Gromacs uses units of kJ mol^-1 nm^-2.

-Justin

>
> thanks for the fast answere.
>
> kind regards
> Bjoern Olausson
>
> --
> Bjoern Olausson
> Martin-Luther-University Halle-Wittenberg
> Institute of Biochemistry/Biotechnology
> AG Molecular Modeling
> 06099 Halle, Germany
> Phone: +49-345-5524863
> Fax: +49-345-5527011
>



========================================

Justin A. Lemkul
Graduate Research Assistant
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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----- End forwarded message -----



========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================