[gmx-users] get a top file to run md simulation

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 13 15:40:05 CET 2009

oguz gurbulak wrote:
> Dear Users,
> I'm trying to obtain .gro and top files successfuly for my n-alkanes 
> molecules and want to run md simulations both using oplsaa and Gromos96 
> force fields seperately. Then I will compare the results of two md runs. 
> I think that I can generate itp files for Gromos96 force fields  using 
> prodgr server and use them for md. But I sholud  write itp files for 
> each molecules I want to use for oplsaa . Lets say that I produced itp 
> files, How can I use for example two different itp files and generate a 
> top file like in below. I'm confused about this. Could you give me the 
> information about this procedure ?

I don't understand your question.  If you create the two .itp files, you do 
exactly as is shown below - that's your topol.top.  Then include any other 
necessary molecule types you may need (water, ions, etc.)

Perhaps you should try running through some simple tutorials (typically 
involving proteins) to understand the topology #include mechanism and overall 
construction.  There are several linked from the wiki.


> Sincerely
> #include "ffoplsaa.itp"
> #include "molecule_A.itp"
> #include "molecule_B.itp"
> [ system ]
> packmol system
> [ molecules ]
> Molecule_A    N
> Molecule_B    N
> ------------------------------------------------------------------------
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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