gromacs.org_gmx-developers Digest, Vol 125, Issue 17

[Ghadafi]

How adding force field in gromacs?

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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
To: Discussion list for GROMACS development
Subject: [gmx-developers] pull-geometry=position is no longer
supported
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: [phone].
------------------------------
Message: 2
Date: Wed, 24 Sep 2014 17:59:04 +0200
Subject: Re: [gmx-developers] pull-geometry=position is no longer
supported
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,
commit cc819af8c6691d70a84f76ae622f604f83ebf440
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

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
Subject: Re: [gmx-developers] pull-geometry=position is no longer
supported
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,

Thanks, then I will try to implement a workaround in gmx wham for
dealing with old input.

commit cc819af8c6691d70a84f76ae622f604f83ebf440
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

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: [phone].
------------------------------
Message: 4
Date: Wed, 24 Sep 2014 18:24:30 +0200
Subject: Re: [gmx-developers] pull-geometry=position is no longer
supported
Content-Type: text/plain; charset=windows-1252; format=flowed

Hi,
This is as expected. I guess it didn't show up in the release notes,

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
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
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

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
Subject: Re: [gmx-developers] pull-geometry=position is no longer
supported
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,

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
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
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

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: [phone].
------------------------------
Message: 6
Date: Wed, 24 Sep 2014 19:44:03 +0200
Subject: Re: [gmx-developers] pull-geometry=position is no longer
supported
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,

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.

/* 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
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
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

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: [phone].
------------------------------
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End of gromacs.org_gmx-developers Digest, Vol 125, Issue 17
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