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Reverse Transformation
- bt12d026
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10 years 8 months ago #1841
by bt12d026
Reverse Transformation was created by bt12d026
Dear All,
I am trying to reverse transform my CG system. I am following the tutorial as well as the publication by Rzepiela et al. My system has protein and lipids. When I do the the second step of SA, with SA time parameters 0 1.5 0 1.5 0 1.5, its terminating with the following error.
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 4913 ]
What should be the possible source of error?
Thanks a lot for your valuable time and concern
I am trying to reverse transform my CG system. I am following the tutorial as well as the publication by Rzepiela et al. My system has protein and lipids. When I do the the second step of SA, with SA time parameters 0 1.5 0 1.5 0 1.5, its terminating with the following error.
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 4913 ]
What should be the possible source of error?
Thanks a lot for your valuable time and concern
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- Clement
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10 years 8 months ago #1842
by Clement
Replied by Clement on topic Reverse Transformation
If I'm not mistaken, this type of error should be avoided by the tweaked version of GROMACS... Which version of mdrun are you using?
Oh! And since we got that out... If it's for only one frame (not a trajectory), maybe you could try with the new initram tool, available at: http://md.chem.rug.nl/cgmartini/index.php/back .
Oh! And since we got that out... If it's for only one frame (not a trajectory), maybe you could try with the new initram tool, available at: http://md.chem.rug.nl/cgmartini/index.php/back .
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- bt12d026
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10 years 8 months ago #1843
by bt12d026
Replied by bt12d026 on topic Reverse Transformation
Sir, I am using the tweaked version of Gromacs.
Could you please tell me how to use the backward tool? When I try to execute it,
$python backward.py -f cg-lipid-protein.pdb
The output is
Residues defined for transformation from martini to gromos:
Traceback (most recent call last):
File "backward.py", line 821, in <module>
raise ValueError, "Unknown residue: %sn"%resn
ValueError: Unknown residue: PPC
Since my system has PPC lipids, how to add its mapping info to Mapping directory?
Could you please tell me how to use the backward tool? When I try to execute it,
$python backward.py -f cg-lipid-protein.pdb
The output is
Residues defined for transformation from martini to gromos:
Traceback (most recent call last):
File "backward.py", line 821, in <module>
raise ValueError, "Unknown residue: %sn"%resn
ValueError: Unknown residue: PPC
Since my system has PPC lipids, how to add its mapping info to Mapping directory?
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- bt12d026
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10 years 8 months ago #1844
by bt12d026
Replied by bt12d026 on topic Reverse Transformation
I forgot to check the initram tool. I'll check and try myself. If I have some problem, I'll get back to you Sir.
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- Clement
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10 years 8 months ago #1845
by Clement
Replied by Clement on topic Reverse Transformation
The initram tool is using the backward python script; you'll have the same error. I forwarded your message to the maintainer of the script. He'll come back at you soon.
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- bt12d026
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10 years 8 months ago #1846
by bt12d026
Replied by bt12d026 on topic Reverse Transformation
Yes, initram is throwing the same error sir. Why simulated annealing with the tweaked ver. of Gromacs is giving trouble?
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- tsjerk
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10 years 8 months ago #1847
by tsjerk
Replied by tsjerk on topic Reverse Transformation
Rzepielas method works, but requires quite a bit of work to get things done.
For the new method, you can only convert things for which a mapping definition is given in the directory Mapping, for the force field you want to map to. The language is pretty straightforward. Find the lipid that looks most like yours, see how it is put together and modify it to match your problem.
Cheers,
Tsjerk
For the new method, you can only convert things for which a mapping definition is given in the directory Mapping, for the force field you want to map to. The language is pretty straightforward. Find the lipid that looks most like yours, see how it is put together and modify it to match your problem.
Cheers,
Tsjerk
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