[gmx-developers] pull-geometry=position is no longer supported

[Berk Hess]

On 09/24/2014 07:44 PM, David van der Spoel wrote:
> On 2014-09-24 19:14, David van der Spoel wrote:
>> On 2014-09-24 18:24, Berk Hess wrote:
>>> On 09/24/2014 06:20 PM, David van der Spoel wrote:
>>>> On 2014-09-24 17:59, Berk Hess wrote:
>>>>> Hi,
>>>>>
>>>>> This is as expected. I guess it didn't show up in the release notes,
>>>>> since it's not in the headline of the commit:
>>>>
>>>>
>>>> Thanks, then I will try to implement a workaround in gmx wham for
>>>> dealing with old input.
>>
>> Just realized that the fatal error is in tpxio.c, so I do no see a
>> possibility to build a workaround for that.
> Unless I move it to mdrun. Right now the code is like this:
>
>         /* epullgPOS for position pulling, before epullgDIRPBC was 
> removed */
>         if (pull->eGeom == epullgDIRPBC)
>         {
>             gmx_fatal(FARGS, "pull-geometry=position is no longer 
> supported");
>         }
>         if (pull->eGeom > epullgDIRPBC)
>         {
>             pull->eGeom -= 1;
>         }
>
> would it be OK to remove both statements, and implement the gmx_fatal 
> in mdrun? Then gmx wham can do something intelligent. Maybe.
That would also require the enum to be changed back.
But I don't see the point. In 5.0 mdrun no longer supports pull-geometry 
= position, so there is no point in supporting it in g_wham of version 
5.0. This would only be useful for processing 4.6 pull xvg files with a 
5.0 g_wham.

For most setup you should be able to use the origin option together with 
geometry=distance to get the same results. Then g_wham should work for 
5.0 input and output. Even the g_wham 5.0 could work with 4.6 
geometry=position output when the number of column matches.

Cheers,

Berk
>
>
>>
>>> Maybe you could also have a look at a pull change for master, which
>>> extends the work of this commit:
>>> https://gerrit.gromacs.org/#/c/3947/
>>>
>>> I asked Jochen if he could update g_wham, but he didn't respond (yet).
>>>
>> Do you have a test data set?
>> Then please send it to me off-list.
>>
>>
>>> Cheers,
>>>
>>> Berk
>>>>
>>>>>
>>>>> commit cc819af8c6691d70a84f76ae622f604f83ebf440
>>>>> Author: Berk Hess <hess at kth.se>
>>>>> Date:   Tue Nov 26 09:41:01 2013 +0100
>>>>>
>>>>>      Removed restriction of one reference pull group
>>>>>
>>>>>      The pull code now uses separate pull groups and coordinates,
>>>>>      which removes any restriction on group pairing.
>>>>>      The pull geometry "position" has been removed, but the origin
>>>>>      option replaces this functionaliy in case of an absolute
>>>>> reference.
>>>>>      Removed triple use of the init option.
>>>>>      Refs #1346
>>>>>
>>>>>      Change-Id: I90736ac6b6f18e3bf26a344072172a69627566e9
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Berk
>>>>>
>>>>> On 24/09/14 17:38 , David van der Spoel wrote:
>>>>>> We're getting this error when running gmx wham in 5.0 with runs
>>>>>> produced in 4.6. Is that as expected or is this a bug in 5.0? I
>>>>>> couldn't find this in the release notes.
>>>>>
>>>>
>>>>
>>>
>>
>>
>
>