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

[Thomas Evangelidis]

Indeed  :-)


2011/4/16 João Henriques <joao.henriques.32353 at gmail.com>

> 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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>
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-- 

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

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang at bioacademy.gr

          tevang3 at gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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