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

[David van der Spoel]

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.


>
>> 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.
>>>>
>>>
>>>
>>
>
>


-- 
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