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Bug #1655

g_membed and box type

Added by Ozge Yoluk almost 5 years ago.

Status:
New
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

GMX version 5.0.2

g_membed runs into problems when using triclinic box. When the molecule is centered in the triclinic box (4gmembed.pdb) I get 'Water molecule starting at X cannot be settled error'. Translating the box fixes this issue (4gmembed_translate-2-0-0). Initial guess is gmembed assumes a rectangular box and treats the system accordingly.

membed.tpr file is generated from 4gmembed_translate-2-0-0
membed_not_working.tpr is generated from 4gmembed.pdb (error pops up after step 500, and ends with a segmentation fault)

A box of similar size with the same system but rectangular runs without a problem.

4gmembed.pdb (16.9 MB) 4gmembed.pdb not working, protein centered in triclinic box Ozge Yoluk, 12/09/2014 01:17 PM
4gmembed_translate-2-0-0.pdb (16.9 MB) 4gmembed_translate-2-0-0.pdb working pdb file Ozge Yoluk, 12/09/2014 01:17 PM
membed.dat (487 Bytes) membed.dat Ozge Yoluk, 12/09/2014 01:18 PM
gmembed.mdp (11.1 KB) gmembed.mdp Ozge Yoluk, 12/09/2014 01:18 PM
membed.tpr (14.1 MB) membed.tpr working tpr file Ozge Yoluk, 12/09/2014 01:19 PM
membed_not_working.tpr (14.1 MB) membed_not_working.tpr Ozge Yoluk, 12/09/2014 01:27 PM
gmembed_error.txt (1.3 KB) gmembed_error.txt Ozge Yoluk, 12/09/2014 01:32 PM

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