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

[Justin A. Lemkul]

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>> 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>>> 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/> | (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

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