[gmx-users] problems with tutor version 4.5.1

[Justin A. Lemkul]

Christian Schaffner wrote:
> Hi guys
> 
> Are the tutorials from /share/gromacs/tutor still up to date?
> 
> In GMXDEMO, I first had to make the file demo executable first by
> chmod +x demo
> 
> Then, in Step 3, when running pdb2gmx, the executable window only shows
> up very quickly and the demo-program hangs. Probably, this is due to the
> (new?) choices that need to be made in the program.
> 

Yes, there are more interactive choices, most notably water model selection.

> 
> When trying to run
> grompp -v
> in the subdirectory water, I get
> -------------------------------------------------------
> Program grompp, VERSION 4.5.1
> Source code file:
> /ufs/schaffne/export/bio/gromacs-4.5.1/src/kernel/grompp.c, line: 1301
> 
> Fatal error:
> Too many warnings (1), grompp terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> I can use
> grompp -v -maxwarn 3
> which then works fine.
> 

Probably related to the presence of unsupported old options.

> 
> When running
> grompp -v
> in subdirectory mixed, I get
> -------------------------------------------------------
> Program grompp, VERSION 4.5.1
> Source code file:
> /ufs/schaffne/export/bio/gromacs-4.5.1/src/gmxlib/gmxcpp.c, line: 248
> 
> Fatal error:
> Topology include file "methanol.itp" not found
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> which I don't know how to fix.
> 

This is likely due to the complete re-organization of the force fields, which 
have a new subdirectory structure.

If you're looking for tutorial material, the Gromacs site has far more detailed 
information:

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

Nonetheless, this stuff should be fixed, I suppose.

-Justin

> 
> Thanks for some help,
> Chris
> 

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

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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