[gmx-developers] Re: bug in h-bond constraints for shake?
Shirts, Michael (mrs5pt)
mrs5pt at eservices.virginia.edu
Thu Feb 3 15:05:53 CET 2011
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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