[gmx-users] top file

[Justin A. Lemkul]

jojo J wrote:
> Hello,
> 
> Thank you for your answer. I mean if I need to go back and comment those 
> lines. (if the results are trusted ..actually I forgot to comment the 
> lines..)
> 
> 

There's no need to comment out lines referring to solvent, ions, etc if they are 
not present.  These statements just include extra (unnecessary) information. 
For more, see Chapter 5 of the Gromacs manual, and the short version of the 
topic here to understand what's going on:

http://www.gromacs.org/Documentation/Include_File_Mechanism

-Justin

> 
> On 8 July 2010 23:10, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     jojo J wrote:
> 
>         Helllo,
> 
>         I got top file using pdb2gmx but I did not comment unnecessary
>         lines at the end of the file ( no water in my system
>         ). With this top file I energy minimized my system. I wanted to
>         know if I am fine ...?
> 
> 
>     Depends on your definition of "fine."  Do you mean to ask if you've
>     done the procedure right, or if the results should be trusted, or
>     something else?
> 
>     -Justin
> 
>         Thank you,
> 
> 
>     -- 
>     ========================================
> 
>     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

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