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Bug #241

Pedantic loss of generality in gromacs 4.0 vs. 3.3.1

Added by Chris Neale about 12 years ago. Updated almost 12 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

This is actually for gromacs 4.0, but that option did not exist in the pull down above so I chose 4.0 RC1. This was on an opteron running HP Linux XC 3.1.

I made a box of water and pdb2gmx gave me a .top file that listed

[ molecules ]
; Compound #mols
SOL 895

grompp worked fine on this system.

I then modified that section to look like this

[ molecules ]
; Compound #mols
SOL 100
SOL 795

and I got the following error:

Program grompp, VERSION 4.0
Source code file: grompp.c, line: 352

Fatal error:
number of coordinates in coordinate file (out.gro, 2685)
does not match topology (topol.top, 300)

####

Obviously this is not a huge problem, but it is non-intuitive. I discovered this based on a box with a number of proteins in it, but verified it with water to let you test it easily. You could probably take any system that you have and split it like this to get a similar error.

Chris.

History

#1 Updated by Berk Hess almost 12 years ago

I have fixed this bug for 4.0.1.

Berk

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