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Sire Developers

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julien, … Antonia Mey4

3/31/15

Export to github

Hi Chrisopher, Ok I'll add you to michellab and start adding it to github. Best, Antonia On

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Export to github

Hi Chrisopher, Ok I'll add you to michellab and start adding it to github. Best, Antonia On

3/31/15

Stefano Bosisio, julien3

3/16/15

Print bond energies

Great Julien! It works and I can adapt for my purpose Thanks a lot! Best wishes, Stefano

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Print bond energies

Great Julien! It works and I can adapt for my purpose Thanks a lot! Best wishes, Stefano

3/16/15

julien, Christopher Woods3

3/9/15

Benchmarks for amber topology parser

Hi Chris, Thanks for the comments. I think the problem for Hannes is that his goal is to process

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Benchmarks for amber topology parser

Hi Chris, Thanks for the comments. I think the problem for Hannes is that his goal is to process

3/9/15

julien, Christopher Woods2

10/23/14

changes in behavior of iterations over molecules container

Hi Julien, The problem was caused by the change in behaviour of QHash from Qt4 to Qt5. In the old

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changes in behavior of iterations over molecules container

Hi Julien, The problem was caused by the change in behaviour of QHash from Qt4 to Qt5. In the old

10/23/14

julien, Christopher Woods6

10/23/14

Debugging rigid body code. Error with matrix multiplication code?

Hi Julien, I think that it goes a little deeper than that. The problem is that 'orient' and

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Debugging rigid body code. Error with matrix multiplication code?

Hi Julien, I think that it goes a little deeper than that. The problem is that 'orient' and

10/23/14

julien, Christopher Woods10

10/8/14

sire build issues

Hi Julien, Yes, "illegal instruction" errors are caused when AVX code is run on a processor

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sire build issues

Hi Julien, Yes, "illegal instruction" errors are caused when AVX code is run on a processor

10/8/14

julien, Christopher Woods2

10/7/14

building sire on CentOS 6.5

Hi Julien, zlib can be a bit of a pain. Qt compiles and includes its own version of zlib when it is

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building sire on CentOS 6.5

Hi Julien, zlib can be a bit of a pain. Qt compiles and includes its own version of zlib when it is

10/7/14

julien, Christopher Woods2

9/17/14

Clean docstrings

Hi Julien, No, I am sorry that you can't hide all of these functions. These are functions from

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Clean docstrings

Hi Julien, No, I am sorry that you can't hide all of these functions. These are functions from

9/17/14

julien, Christopher Woods2

9/17/14

Hi Julien, Yes, you can run the tests one at a time. To do this, just run the test using $SIRE/bin/

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Hi Julien, Yes, you can run the tests one at a time. To do this, just run the test using $SIRE/bin/

9/17/14

julien, Christopher Woods19

8/19/14

sommmd & analyse_freenrg integration

Hi Julien, I've been taking a look at your question around various distractions and am not sure

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sommmd & analyse_freenrg integration

Hi Julien, I've been taking a look at your question around various distractions and am not sure

8/19/14

julien, Christopher Woods2

8/19/14

pip bundle in latest code

Hi Julien, Yes - pip should be installed and bundled but there is a bug with my install scripts that

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pip bundle in latest code

Hi Julien, Yes - pip should be installed and bundled but there is a bug with my install scripts that

8/19/14

julien, Gaetano Calabró5

7/25/14

Generating python wrappers

Hi Julien, go to this page https://github.com/gccxml/gccxml and click “Download Zip” on the right of

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Generating python wrappers

Hi Julien, go to this page https://github.com/gccxml/gccxml and click “Download Zip” on the right of

7/25/14

julien, Gaetano Calabró4

7/24/14

Sire and OpenMM energies 1,4 scaling factor unity

Hi Gaetano, Commit your code changes, even if the energies do not match with Sire. Write comments in

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Sire and OpenMM energies 1,4 scaling factor unity

Hi Gaetano, Commit your code changes, even if the energies do not match with Sire. Write comments in

7/24/14

julien, Christopher Woods3

7/23/14

Agreement single point energies sander vs Sire

Phew. Just got back from the group excursion at the EMBO meeting to read your first email and thought

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Agreement single point energies sander vs Sire

Phew. Just got back from the group excursion at the EMBO meeting to read your first email and thought

7/23/14

julien, Gaetano Calabró2

7/20/14

Generating python wrappers on recent version of the code

Hi Julien, you cannot use Ubuntu 12.04 to generate the wrapper with the latest version of Sire. You

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Generating python wrappers on recent version of the code

Hi Julien, you cannot use Ubuntu 12.04 to generate the wrapper with the latest version of Sire. You

7/20/14

julien, Christopher Woods4

4/14/14

Request for code change in SireMM/internalparameters.cpp

Hi Julien, I agree - the first option is better (adding an intrascale property in Amber and setting

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Request for code change in SireMM/internalparameters.cpp

Hi Julien, I agree - the first option is better (adding an intrascale property in Amber and setting

4/14/14

hannes....@gmail.com, Christopher Woods4

3/28/14

possible problem with Sire.IO.Amber.readCrdTop()

Many thanks, Chris. This factor confused me because Gromacs for example wants sigma while the

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possible problem with Sire.IO.Amber.readCrdTop()

Many thanks, Chris. This factor confused me because Gromacs for example wants sigma while the

3/28/14

Christopher, george gerogiokas8

4/17/13

Re: Centos Compilation Errors:

Hi Chris, Yes, that's right I had thought I turned it on but I didn't. -- Using Qt version

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Re: Centos Compilation Errors:

Hi Chris, Yes, that's right I had thought I turned it on but I didn't. -- Using Qt version

4/17/13

julien, Christopher Woods4

1/22/13

Reloading a restart file fails if some molecule properties are removed before writing the restart

Hi Julien, Excellent news that the restart file is smaller. It is nice to know that Sire is behaving

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Reloading a restart file fails if some molecule properties are removed before writing the restart

Hi Julien, Excellent news that the restart file is smaller. It is nice to know that Sire is behaving

1/22/13

julien, Christopher Woods2

1/8/13

You may have a forcefield expression that contains a free term that is not dependent on a forcefield component.

Hi Julien, The debug message occurs when the code sees that an energy expression contains a constant

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You may have a forcefield expression that contains a free term that is not dependent on a forcefield component.

Hi Julien, The debug message occurs when the code sees that an energy expression contains a constant

1/8/13

julien, Christopher Woods3

11/28/12

Exposing MoleculeData to Python

Hi Julien, Your solution is the "correct" way of initializing the coordinates. I

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Exposing MoleculeData to Python

Hi Julien, Your solution is the "correct" way of initializing the coordinates. I

11/28/12

julien, Christopher Woods4

8/24/12

Different behavior of Sire script when executed by python or ipython

Hi Julien, That is very strange, as the RunTime warnings should not affect the C++ code (as each

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Different behavior of Sire script when executed by python or ipython

Hi Julien, That is very strange, as the RunTime warnings should not affect the C++ code (as each

8/24/12

6/19/12

Custom system properties

Hi Chris, I was wondering if you could help with this problem. I would like to write a python code

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Custom system properties

Hi Chris, I was wondering if you could help with this problem. I would like to write a python code

6/19/12

Gaetano Calabrò, Christopher Woods2

3/15/12

Periodic Box Dimensions - OpenMM

Dear Gaetano, You are updating the space in the right way. It has to be done via the "system.

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Periodic Box Dimensions - OpenMM

Dear Gaetano, You are updating the space in the right way. It has to be done via the "system.

3/15/12

Gaetano Calabrò, Christopher3

2/22/12

Sire extension using OpenMM

Hi Christopher, Thanks a lot for your prompt reply. I was able to pass back my data following your

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Sire extension using OpenMM

Hi Christopher, Thanks a lot for your prompt reply. I was able to pass back my data following your

2/22/12

julien, Christopher Woods6

11/22/11

python MM wrappers compilation error

Hi Julien, The problem is that the generator of the python wrappers is unable to decide how to handle

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python MM wrappers compilation error

Hi Julien, The problem is that the generator of the python wrappers is unable to decide how to handle

11/22/11

4/19/11

compilation error gcc 4.5.2

Issue reported on google code as well. Observed on a ubuntu 11.04 beta2 that comes with a recent gcc

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compilation error gcc 4.5.2

Issue reported on google code as well. Observed on a ubuntu 11.04 beta2 that comes with a recent gcc

4/19/11

julien, Christopher Woods2

2/10/11

Bug in Velocity3D

Hi Julien, Yes - it is a bug in the copy constructor for Vector3D. Thanks for spotting it :-). The

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Bug in Velocity3D

Hi Julien, Yes - it is a bug in the copy constructor for Vector3D. Thanks for spotting it :-). The

2/10/11

11/10/10

Possible bug with system.properties()

Hi Chris, There is a problem with the property "alpha". The following is an ipython session

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Possible bug with system.properties()

Hi Chris, There is a problem with the property "alpha". The following is an ipython session

11/10/10

julien, Christopher Woods6

10/22/10

Returning Space

Hi Julien, You've included the SireMol/moleditor.h and SireMol/atomeditor.h header files in amber

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Returning Space

Hi Julien, You've included the SireMol/moleditor.h and SireMol/atomeditor.h header files in amber

10/22/10

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