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

[João Henriques]

With all due respect, this is clearly a RT*M moment.

* = F

Joao Henriques

On Fri, Apr 15, 2011 at 1:03 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ========================================
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