[gmx-developers] gromacs.org_gmx-developers Digest, Vol 125, Issue 17

Ghadafi ghadafimuh at hotmail.com
Thu Sep 25 00:47:28 CEST 2014


How adding force field in gromacs?

gromacs.org_gmx-developers-request at maillist.sys.kth.se wrote:

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>Today's Topics:
>
>   1. pull-geometry=position is no longer supported
>      (David van der Spoel)
>   2. Re: pull-geometry=position is no longer supported (Berk Hess)
>   3. Re: pull-geometry=position is no longer supported
>      (David van der Spoel)
>   4. Re: pull-geometry=position is no longer supported (Berk Hess)
>   5. Re: pull-geometry=position is no longer supported
>      (David van der Spoel)
>   6. Re: pull-geometry=position is no longer supported
>      (David van der Spoel)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Wed, 24 Sep 2014 17:38:27 +0200
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>To: Discussion list for GROMACS development
>	<gmx-developers at gromacs.org>
>Subject: [gmx-developers] pull-geometry=position is no longer
>	supported
>Message-ID: <5422E573.8090608 at xray.bmc.uu.se>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>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
>
>
>------------------------------
>
>Message: 2
>Date: Wed, 24 Sep 2014 17:59:04 +0200
>From: Berk Hess <hess at kth.se>
>To: gmx-developers at gromacs.org
>Subject: Re: [gmx-developers] pull-geometry=position is no longer
>	supported
>Message-ID: <5422EA48.60203 at kth.se>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>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:
>
>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.
>
>
>
>------------------------------
>
>Message: 3
>Date: Wed, 24 Sep 2014 18:20:07 +0200
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>To: gmx-developers at gromacs.org
>Subject: Re: [gmx-developers] pull-geometry=position is no longer
>	supported
>Message-ID: <5422EF37.5020802 at xray.bmc.uu.se>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>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.
>
>>
>> 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
>
>
>------------------------------
>
>Message: 4
>Date: Wed, 24 Sep 2014 18:24:30 +0200
>From: Berk Hess <hess at kth.se>
>To: gmx-developers at gromacs.org
>Subject: Re: [gmx-developers] pull-geometry=position is no longer
>	supported
>Message-ID: <5422F03E.40309 at kth.se>
>Content-Type: text/plain; charset=windows-1252; format=flowed
>
>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.
>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).
>
>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.
>>>
>>
>>
>
>
>
>------------------------------
>
>Message: 5
>Date: Wed, 24 Sep 2014 19:14:44 +0200
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>To: gmx-developers at gromacs.org
>Subject: Re: [gmx-developers] pull-geometry=position is no longer
>	supported
>Message-ID: <5422FC04.7000605 at xray.bmc.uu.se>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>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.
>
>> 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
>
>
>------------------------------
>
>Message: 6
>Date: Wed, 24 Sep 2014 19:44:03 +0200
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>To: gmx-developers at gromacs.org
>Subject: Re: [gmx-developers] pull-geometry=position is no longer
>	supported
>Message-ID: <542302E3.7060809 at xray.bmc.uu.se>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>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
>
>
>------------------------------
>
>-- 
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>End of gromacs.org_gmx-developers Digest, Vol 125, Issue 17
>***********************************************************


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