[gmx-users] how to make topol.top file for mixed solution

[Justin A. Lemkul]

cuong nguyen wrote:
> Dear,
> 
> Thanks a lot Justin. I created a box containing mixed solution of 20 
> hexanol molecues and 20 octanol molecules in water. However, when I run 
> grompp and mdrun commands, gromacs noticed errors with the topol.top 
> file for this mixed system.
> 
> So please help me to create a suitable topol.top file to this system.
> 

No one can help you without knowing the exact errors that grompp produced.

-Justin

> Thanks a lot.
> 
> Best regards,
> 
> 
> Cuong
> 
> 2011/11/7 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     Justin A. Lemkul wrote:
> 
> 
> 
>         cuong nguyen wrote:
> 
>             Dear,
> 
>             I would like to create a solution of mix substances (hexanol
>             and octanol) in water. I got top files and gro files of
>             these alcohols from PRODRG server. However I do not know how
>             to mix these top file to create topol.top file for this mixture.
> 
> 
>         Please read the tutorial:
> 
>         http://www.gromacs.org/__Documentation/Tutorials#__Heterogeneous_Systems
>         <http://www.gromacs.org/Documentation/Tutorials#Heterogeneous_Systems>
> 
> 
>     Also possibly useful:
> 
>     http://www.gromacs.org/__Documentation/How-tos/Mixed___Solvents
>     <http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents>
> 
>     -Justin
> 
> 
>     -- 
>     ==============================__==========
> 
>     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
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
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> 
> 
> -- 
> Nguyen Van Cuong
> PhD student - Curtin University of Technology
> Mobile: (+61) 452213981
>  
> 

-- 
========================================

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

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