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Bug #368

grompp perturbs residue numbers

Added by Peter Kasson about 10 years ago. Updated about 10 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Erik Lindahl
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

Created an attachment (id=400)
.gro, .top, .tpr

In both CVS-current (4.0.x release?) and git-current gromacs, if I take a .gro input file with sequentially-numbered residues, run grompp, and then try to make an index file from the result, I get a different residue numbering (atom numbers seem to be preserved). Having trouble tracking down exactly what's going on here, but I'm enclosing example files. Let me know if you want .itp, etc.

example.tgz (4.47 MB) example.tgz .gro, .top, .tpr Peter Kasson, 11/08/2009 05:50 PM

History

#1 Updated by Berk Hess about 10 years ago

Residue number are now determined through the top file.
Moleculetypes with two or more residues retain there numbering,
moleculetypes with one residue continue sequentially.
This has been a request for many years and I think it should
work properly by now.

Berk

#2 Updated by Berk Hess about 10 years ago

I changed the residue numbering.
Gromacs (git master) was supposed to retain the input residue
for molecules with more than 1 residue and continue counting
after the last larger molecule for single residue molecules.
But there might have been a bug in the counting somewhere.
Now the maximum residue number of all molecules is determined first
and counting is continued from there for single residue molecules
(or even multiple-residue molecules with GMX_MAXRESRENUM).

Berk

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