Re: [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 <jalem...@vt.edu <mailto:jalem...@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

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