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Bug #461

crash step.pdb files all get residue #1

Added by Chris Neale over 9 years ago. Updated over 9 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

When the run crashes and step.pdb files are produced, they are all given the same residue number (=1).

You can test this my taking a box of water and setting dt=0.04... it will crash right away.

gpc-f101n084-$ head -n 20 step0b.pdb
TITLE initial coordinates
REMARK THIS IS A SIMULATION BOX
CRYST1 25.000 25.000 25.000 90.00 90.00 90.00 P 1 1
ATOM 1 OW SOL 1 2.250 2.750 9.960
ATOM 2 HW1 SOL 1 2.596 2.577 10.882
ATOM 3 HW2 SOL 1 1.367 2.297 9.844
ATOM 4 OW SOL 1 25.189 3.680 6.470
ATOM 5 HW1 SOL 1 24.375 4.110 6.860
ATOM 6 HW2 SOL 1 24.914 2.952 5.842
ATOM 7 OW SOL 1 5.690 12.750 11.650
ATOM 8 HW1 SOL 1 4.763 12.677 11.280
ATOM 9 HW2 SOL 1 5.803 13.640 12.091
ATOM 10 OW SOL 1 15.550 15.110 7.030
ATOM 11 HW1 SOL 1 14.984 14.950 7.839
ATOM 12 HW2 SOL 1 14.962 15.211 6.227
ATOM 13 OW SOL 1 17.429 6.180 8.559
ATOM 14 HW1 SOL 1 17.764 7.122 8.563
ATOM 15 HW2 SOL 1 17.945 5.640 9.225
ATOM 16 OW SOL 1 11.350 7.030 7.170
ATOM 17 HW1 SOL 1 11.922 7.810 6.918

It's not a big deal, but I noticed this when I went to look at one such file and in VMD I selected resid 1 and I got a selection of the entire box.

Thank you,
Chris.

PS: the version section at the top of bugzilla is out of date. I entered CVS as its the closest, but really this bug is in 4.0.5 and 4.0.7 (at least).

History

#1 Updated by Berk Hess over 9 years ago

I fixed this, both for 4.0.8 (if that will ever be released) and git master.

The version selection should indeed be fixed. We anyhow have to add 4.5beta soon.

Berk

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