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PEG Tutorial - Error Calculating Bond Distances
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4 years 3 months ago - 4 years 3 months ago #8403
by TravisM
PEG Tutorial - Error Calculating Bond Distances was created by TravisM
Hello all,
I am going through the PEG tutorial, and am at the point for calculating bond length/angle distributions of the AA-CG mapped trajectory. I was able to successfuly use gen_indices.py to get the 3 relevant .ndx files. However, when I run gmx distance and send it group bonds_core1 I get this error:
Inconsistency in user input:
Invalid index group references encountered
Group 'bonds_core1' cannot be used in selections, because it contains
negative atom indices and/or references atoms not present (largest allowed
atom index is 0).
The fact that is says "largest allowed atom index is 0" makes me think the issue lies with the trajetory file - However, running gmx angle using the exact same trajectory the command works perfectly.
Any help would be greatly appreciated. Thanks!
I am going through the PEG tutorial, and am at the point for calculating bond length/angle distributions of the AA-CG mapped trajectory. I was able to successfuly use gen_indices.py to get the 3 relevant .ndx files. However, when I run gmx distance and send it group bonds_core1 I get this error:
Inconsistency in user input:
Invalid index group references encountered
Group 'bonds_core1' cannot be used in selections, because it contains
negative atom indices and/or references atoms not present (largest allowed
atom index is 0).
The fact that is says "largest allowed atom index is 0" makes me think the issue lies with the trajetory file - However, running gmx angle using the exact same trajectory the command works perfectly.
Any help would be greatly appreciated. Thanks!
Last edit: 4 years 3 months ago by TravisM.
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4 years 2 months ago #8417
by TravisM
Replied by TravisM on topic PEG Tutorial - Error Calculating Bond Distances
For the sake of future people looking at this question, I thought I would provide a brief update.
I was able to get gmx bond to work correctly if I passed it a .gro file rather than a .xtc file for the trajectory. This was done by using trjconv to create a .gro file from the original .xtc trajectory. It is not clear to me if the output is time averaged or simply bond lengths from the final configuration (I fear it is the latter), but it at least allows you to get a starting histogram for setting up your Take1 parametrization
I was able to get gmx bond to work correctly if I passed it a .gro file rather than a .xtc file for the trajectory. This was done by using trjconv to create a .gro file from the original .xtc trajectory. It is not clear to me if the output is time averaged or simply bond lengths from the final configuration (I fear it is the latter), but it at least allows you to get a starting histogram for setting up your Take1 parametrization
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4 years 2 months ago - 4 years 2 months ago #8423
by riccardo
Replied by riccardo on topic PEG Tutorial - Error Calculating Bond Distances
Thanks for the update on your own question :-)
I think that gmx distance requires a tpr file (in contrast to gmx angle - e.g., see commands listed on the "parametrizing new molecule" tutorial cgmartini.nl/index.php/tutorials-general...ng-new-molecule-gmx5 ) which I see is missing from the line with the gmx distance command in the PEG tutorial ( cgmartini.nl/index.php/tutorials-general...orials-polymers-gmx5 ). Could you try if passing a (CG) tpr fixes it?
I think that gmx distance requires a tpr file (in contrast to gmx angle - e.g., see commands listed on the "parametrizing new molecule" tutorial cgmartini.nl/index.php/tutorials-general...ng-new-molecule-gmx5 ) which I see is missing from the line with the gmx distance command in the PEG tutorial ( cgmartini.nl/index.php/tutorials-general...orials-polymers-gmx5 ). Could you try if passing a (CG) tpr fixes it?
Last edit: 4 years 2 months ago by riccardo.
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4 years 2 months ago #8430
by TravisM
Replied by TravisM on topic PEG Tutorial - Error Calculating Bond Distances
That did it! When I included min.tpr from my first try after creating a .itp file, gmx distance ran without error and I was able to get the correct time-averaged histogram of bond length. Thanks!
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4 years 2 months ago - 4 years 2 months ago #8431
by riccardo
Replied by riccardo on topic PEG Tutorial - Error Calculating Bond Distances
Great!
Definitely, the gromacs error wasn't clear. I will make sure the command in the tutorial gets fixed.
Definitely, the gromacs error wasn't clear. I will make sure the command in the tutorial gets fixed.
Last edit: 4 years 2 months ago by riccardo.
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