[gmx-users] Re: distance restraints for atoms on 2 chains

[Justin A. Lemkul]

Sai Pooja wrote:
> Hi
>  
> This is regarding the pull code.. I have followed your tutorial to get 
> the PMF for distance between 2 atoms using the pull code. I want to know 
> if one can bring the atoms closer rather than pull them apart? I want to 

Set pull_rate < 0.

> start from the maximum distance and then bring them closer to check 
> reversibility. Also, I dont think I can apply it a fixed vector (as in 
> specify the vector from one atom to the other) because I dont think the 
> path will be a straight line.
>  

All pulling is conducted along a vector, either by specifying pull_vec or pull_dim.

-Justin

> Pooja
> 
> On Fri, Apr 1, 2011 at 8:02 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Sai Pooja wrote:
> 
>         The pull tutorial uses npt simulations.. is that required by the
>         algorithm or can one use nvt after the system has been
>         sufficiently equilibrated using npt?
> 
> 
>     Use whatever conditions are appropriate for your system.  Tutorials
>     should not be viewed as the only applicable conditions, merely one
>     such example of what might be done.
> 
>     -Justin
> 
>         On Fri, Apr 1, 2011 at 7:32 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
> 
> 
>            pdb2gmx -chainsep (-merge in 4.0.x and before) should allow
>         you to
>            create a merged [moleculetype] to apply distance restraints.  If
>            you're just trying to use a harmonic potential to define some
>            sampling distance (for US), then distance restraints are not
>            necessary, just apply the pull code.
> 
>            -Justin
> 
>            Sai Pooja wrote:
> 
>                Also, the chains do not diffuse apart in time since they are
>                position restrained(some parts of each chain are ...)
> 
>                On Fri, Apr 1, 2011 at 7:26 PM, Sai Pooja
>         <saipooja at gmail.com <mailto:saipooja at gmail.com>
>                <mailto:saipooja at gmail.com <mailto:saipooja at gmail.com>>
>         <mailto:saipooja at gmail.com <mailto:saipooja at gmail.com>
> 
>                <mailto:saipooja at gmail.com <mailto:saipooja at gmail.com>>>>
>         wrote:
> 
>                   Hi,
>                        I have 5 chains in my Protein. I want to apply
>         distance
>                restraints
>                   for doing Umbrella Sampling for 2 atoms on different
>         chains. Is
>                   there a way to do this since the two chains have separater
>                itp files.
>                        Pooja
> 
>                   --     Quaerendo Invenietis-Seek and you shall discover.
> 
> 
> 
> 
>                --         Quaerendo Invenietis-Seek and you shall discover.
> 
> 
>            --     ========================================
> 
>            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/> <http://vt.edu/> | (540)
>         231-9080 <tel:%28540%29%20231-9080>
>            <tel:%28540%29%20231-9080>
> 
>            http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 
> 
>         -- 
>         Quaerendo Invenietis-Seek and you shall discover.
> 
> 
>     -- 
>     ========================================
> 
>     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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> 
> -- 
> Quaerendo Invenietis-Seek and you shall discover.

-- 
========================================

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

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