normal Problem with Parametrizing new molecule tutorial

  • zidarko
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7 months 2 weeks ago #8161 by zidarko
Hi there,

I've been parametrizing/verifying a force field for a pluronic molecule. I'm following the Parametrizing new molecule tutorial.

I reached the stage where I have to generate target CG distributions by:
"To do this, create a index file with a directive for "[bonds]" containing (multiple) pairs of CG beads, "[angles]" containing triples and "[dihedrals]" quartets. Use g_bond for the bonds, g_angle for angles and dihedrals..."

The problem is that the g_bond command was replaced with 'gmx distance' that has a less than intuitive parameters.

If I run it as suggested by the 'gmx distance' help page:
gmx distance -n temp.ndx -f wpoly-43-16-43-npt-prod-4-mapped.xtc -oallstat -fgroup -s wpoly-43-16-43-npt-prod-init-nowat.gro

The index file contains the relevant directives:
[bonds]
1       2 
2       3 
3       4 
4       5 
5       6 
6       7 
7       8 
8       9 
9       10

What am I missing?

Thanks in advance!

JZidar

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7 months 2 weeks ago #8162 by riccardo
There's a version of the tutorial for GMX > 4.x :
cgmartini.nl/index.php/tutorials-general...ng-new-molecule-gmx5

Going through that should fix your issue.

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7 months 2 weeks ago #8164 by zidarko
Perfect! Works as advertised.

Thank you so much!

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