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Problem with Parametrizing new molecule tutorial
- zidarko
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4 years 9 months ago #8161
by zidarko
Problem with Parametrizing new molecule tutorial was created 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:
What am I missing?
Thanks in advance!
JZidar
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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- riccardo
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4 years 9 months ago #8162
by riccardo
Replied by riccardo on topic Problem with Parametrizing new molecule tutorial
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.
cgmartini.nl/index.php/tutorials-general...ng-new-molecule-gmx5
Going through that should fix your issue.
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- zidarko
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4 years 9 months ago #8164
by zidarko
Replied by zidarko on topic Problem with Parametrizing new molecule tutorial
Perfect! Works as advertised.
Thank you so much!
Thank you so much!
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