Project

General

Profile

Bug #5

gmx benchmark not running missing atom types

Added by Florian Haberl over 14 years ago. Updated over 12 years ago.

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

Description

i checked if r1 compiles, after that i want to run gmxbench 3.0

d.villin and

d.lzm] > grompp -f pme.mdp

mdrun

Back Off! I just backed up md.log to ./#md.log.2#
Reading file topol.tpr, VERSION 3.3_rc1 (single precision)
-------------------------------------------------------
Program mdrun, VERSION 3.3_rc1
Source code file: qmmm.c, line: 292

Fatal error:
atomtype MNH3 does not exist in ffG43a2!

also with d.dppc and d.poly it doesnt work


Back Off! I just backed up md.log to ./#md.log.1#
Reading file topol.tpr, VERSION 3.3_rc1 (single precision)
-------------------------------------------------------
Program mdrun, VERSION 3.3_rc1
Source code file: qmmm.c, line: 292

Fatal error:
atomtype LC3N does not exist in ffG43a2!


I guess wrong choice of force field, perhaps gmxbench 3.0 suite is not working
with new release candidate.

History

#1 Updated by Erik Lindahl over 14 years ago

Hi Florian,

Nope, this is a real bug :-) We merged in some QM-MM code in the last minute that we thought wouldn't
be called, but apparently we were wrong.

#2 Updated by Erik Lindahl over 14 years ago

The QM-MM routine has been disabled in the updated RC1, but the bug still needs to be solved for the
QM-MM to work.

#3 Updated by David van der Spoel over 14 years ago

I assume this means a grompp error?
In that case I can not reproduce it, please be more specific.

#4 Updated by David van der Spoel over 14 years ago

Hi,

sorry about my previous comment, this bug is also fixed in CVS for 3.3 and 4.0 now.

#5 Updated by toper sde over 12 years ago

Created an attachment (id=204)
x1

#6 Updated by toper sde over 12 years ago

Created an attachment (id=205)
x2

#7 Updated by toper sde over 12 years ago

Created an attachment (id=206)
x3

#8 Updated by toper sde over 12 years ago

Created an attachment (id=207)
x4

#9 Updated by toper sde over 12 years ago

Created an attachment (id=208)
x5

#10 Updated by toper sde over 12 years ago

Created an attachment (id=209)
x6

#11 Updated by toper sde over 12 years ago

Created an attachment (id=210)
x7

#12 Updated by toper sde over 12 years ago

Created an attachment (id=211)
x8

#13 Updated by toper sde over 12 years ago

Created an attachment (id=212)
x9

#14 Updated by toper sde over 12 years ago

Created an attachment (id=213)
x10

#15 Updated by Erik Lindahl over 12 years ago

The content of attachment 204 has been deleted by
Erik Lindahl <>
who provided the following reason:

spam

The token used to delete this attachment was generated at 2007-06-25 13:05:49 CET.

#16 Updated by Erik Lindahl over 12 years ago

The content of attachment 213 has been deleted by
Erik Lindahl <>
without providing any reason.

The token used to delete this attachment was generated at 2007-06-25 13:10:16 CET.

#17 Updated by Erik Lindahl over 12 years ago

The content of attachment 205 has been deleted by
Erik Lindahl <>
without providing any reason.

The token used to delete this attachment was generated at 2007-06-25 13:10:26 CET.

#18 Updated by Erik Lindahl over 12 years ago

The content of attachment 212 has been deleted by
Erik Lindahl <>
without providing any reason.

The token used to delete this attachment was generated at 2007-06-25 13:10:39 CET.

#19 Updated by Erik Lindahl over 12 years ago

The content of attachment 211 has been deleted by
Erik Lindahl <>
without providing any reason.

The token used to delete this attachment was generated at 2007-06-25 13:10:50 CET.

#20 Updated by Erik Lindahl over 12 years ago

The content of attachment 210 has been deleted by
Erik Lindahl <>
without providing any reason.

The token used to delete this attachment was generated at 2007-06-25 13:11:04 CET.

#21 Updated by Erik Lindahl over 12 years ago

The content of attachment 209 has been deleted by
Erik Lindahl <>
without providing any reason.

The token used to delete this attachment was generated at 2007-06-25 13:11:14 CET.

#22 Updated by Erik Lindahl over 12 years ago

The content of attachment 208 has been deleted by
Erik Lindahl <>
without providing any reason.

The token used to delete this attachment was generated at 2007-06-25 13:11:23 CET.

#23 Updated by Erik Lindahl over 12 years ago

The content of attachment 207 has been deleted by
Erik Lindahl <>
without providing any reason.

The token used to delete this attachment was generated at 2007-06-25 13:11:33 CET.

#24 Updated by Erik Lindahl over 12 years ago

The content of attachment 206 has been deleted by
Erik Lindahl <>
without providing any reason.

The token used to delete this attachment was generated at 2007-06-25 13:11:52 CET.

Also available in: Atom PDF