Re: [gmx-users] Dihedral restraints in 4.6 vs 4.5.X

[Per Larsson]

Thanks  - I have filed issue #1194 and assigned it to David.
http://redmine.gromacs.org/issues/1194

Let me know if there is anything else that is needed. I could take a shot at 
myself, and will play around with it, but I don't know the details of the 
symtab in any detail, unfortunately. 

15 mar 2013 kl. 19:51 skrev David van der Spoel:
>> 
>> Taking away the restraint allows me to start the run in 4.6.1, and also 
>> reformatting the [ dihedral_restraint ] section to comply with 4.6 works.
>> Is this a know issue, am I missing something obvious, or should I file an 
>> issue on redmine?
> 
> redmine please.
> 
>> 
>> Thanks
>> /Per--
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> 
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> -- 
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Re: [gmx-users] Dihedral restraints in 4.6 vs 4.5.X

[David van der Spoel]

On 2013-03-15 15:31, Per Larsson wrote:

Hi

I anyone aware of any issue starting simulations with 4.6 (or 4.6.1) from a 
4.5.X-tpr file with dihedral restraints?
I'm unsuccessful in making them start.

To investigate further, I created a small dialanine peptide in vacuum, with a 
dihedral restraint.

Here's the details:

Making a 4.5.5 tpr with a dihedral restraint
$grompp -f md.mdp -c conf.gro -p topol.top -o md.tpr

Checking that it is there:
$gmxdump -s md.tpr |grep DIHRE
Reading file md.tpr, VERSION 4.5.5 (single precision)
 functype[166]=DIHRES, label=0, power=   1 phi= 1.2000e+02, dphi= 
3.e+01, kfac= 1.e+00)



Now running this in 4.5.5 works fine, but starting it in 4.6 (or 4.6.1) gives 
me an error.

$ /Users/per/source/gromacs-4.6.1/build/src/kernel/mdrun -v -deffnm md
Reading file md.tpr, VERSION 4.5.5 (single precision)

---
Program mdrun, VERSION 4.6.1
Source code file: /Users/per/source/gromacs-4.6.1/src/gmxlib/symtab.c, line: 136

Fatal error:
symtab get_symtab_handle 1051260126 not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Taking away the restraint allows me to start the run in 4.6.1, and also 
reformatting the [ dihedral_restraint ] section to comply with 4.6 works.
Is this a know issue, am I missing something obvious, or should I file an issue 
on redmine?


redmine please.



Thanks
/Per--
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
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