[gmx-developers] Re: bug in h-bond constraints for shake?

[Shirts, Michael (mrs5pt)]

Hi, all-

The fundamental issue here is that shake blocks have to be consecutive in
the structure, i.e., if constraint hbonds are set, then:

*****************************************

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass
     1  opls_157B      1   ETH    CB      1     0.6850    12.0110
     5   opls_154      1   ETH    OG      2    -0.9830    15.9994
     2   opls_140      1   ETH   HB1      3    -0.1400     1.0080
     3   opls_140      1   ETH   HB2      4    -0.1400     1.0080
     4   opls_140      1   ETH   HB3      5    -0.1400     1.0080
     6   opls_155      1   ETH    HG      6     0.7180     1.0080

*****************************************

Fails with error:

*****************************************

Double sids (0, 1) for atom 1
Double sids (0, 1) for atom 2
Double sids (0, 1) for atom 3
Double sids (0, 1) for atom 4
Double sids (0, 1) for atom 5

-------------------------------------------------------
Program mdrun_d, VERSION 4.5-beta4-dev-20110127-13f95-dirty
Source code file: 
/Users/mrshirts/work/gromacs_allv/git/gromacs/src/gmxlib/invblock.c, line:
79

Fatal error:
Double entries in block structure. Item 6 is in blocks 1 and 0
 Cannot make an unambiguous inverse block.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
*****************************************

Whereas:

*****************************************

[ atoms ]
     1  opls_157B      1   ETH    CB      1     0.6850    12.0110
     2   opls_140      1   ETH   HB1      2    -0.1400     1.0080
     3   opls_140      1   ETH   HB2      3    -0.1400     1.0080
     4   opls_140      1   ETH   HB3      4    -0.1400     1.0080
     5   opls_154      1   ETH    OG      5    -0.9830    15.9994
     6   opls_155      1   ETH    HG      6     0.7180     1.0080

will run fine.

Since a lot of parameterization programs output all heteroatoms then all
hydrogens, I think it would be good to have shake be able to figure out the
constraint groups from the bonds, not from the topology.  I realize this may
be difficult, and would be willing to implement it if given some pointers; I
tried at one point and gave up trying to figure it out how to fix this after
a couple of hours.

I'm happy to post simple sample files if someone else wants to do it, of
course!

Best,
~~~~~~~~~~~~
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434)-243-1821


> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Date: Thu, 3 Feb 2011 02:36:26 -0500
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Subject: Re: [gmx-developers] Re: bug in h-bond constraints for shake?
> 
> On 2011-02-02 23.16, Dan Vanatta wrote:
>> 
>> Michael Shirts<mrshirts<at>  gmail.com>  writes:
>> 
>>> -------------------------------------------------------
>>> Program mdrun, VERSION 4.0.99_development_20090927
>>> Source code file: invblock.c, line: 79
>>> 
>>> Fatal error:
>>> Double entries in block structure. Item 35 is in blocks 1 and 0
>>>   Cannot make an unambiguous inverse block.
>>> For more information and tips for trouble shooting please check the
>>> GROMACS website at
>>> http://www.gromacs.org/Documentation/Errors
>>> -------------------------------------------------------
>> 
>> Hi,
>> 
>> I'm still running into this issue using gromacs 4.5.2, did anyone ever figure
>> out why this was happening?
>> 
>> Best,
>> Dan
>> 
>> 
>> 
>> 
>> 
> Please file a bug on redmine.gromacs.org and upload files necessary to
> reproduce (incl. grompp input).
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> -- 
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