[gmx-users] Adding water to protein to start the simulation process

[Justin A. Lemkul]

Monisha Hajra wrote:
> Hi Justin,
> 
> I am trying to follow the protocol only.
>  
> More than the Gromacs own website, I find 
> http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html#production link is 
> more useful.
> 

Clearly.  This is one of many tutorials linked from the site I posted before.

> However, I am stuck at one step which is mentioned :
> http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis.html
> 
> I am not able to understand how to create traj.trr, traj.xtc and 
> ener.edr file. Remaining all is self explained in the previous link.
> 

These files are output by mdrun, i.e. actually running a simulation.

-Justin

> Really appreciate any help.
> 
> Regards
> Monisha
> 
> 
> On Fri, Apr 15, 2011 at 8:06 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Monisha Hajra wrote:
> 
>         Hi User,
> 
>         I have a protein which I have modeled by Homology modelling. The
>         modeled protein has no water molecules in its surrounding
>         environment.
> 
>         How should I add water molecule so that I can start the
>         simulation process?
> 
> 
>     Please refer to the abundant tutorial material on the website:
> 
>     http://www.gromacs.org/Documentation/Tutorials#General_GROMACS_Use
>     http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
> 
>     -Justin
> 
>         Regards
>         Monisha
> 
> 
>     -- 
>     ========================================
> 
>     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
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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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

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