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crystallography and molecular dynamics packages in synaptic
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A place to discuss scientific and mathematics software for Ubuntu or linux in general. Questions and comments from all academic and research disciplines are welcome.
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March 3rd, 2008 #1
nkamesh
First Cup of Ubuntu
Join Date: Mar 2008
Beans: 2 crystallography and molecular dynamics packages in synaptic
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hi
I am a newbie to the linux world and recently installed ubuntu. Its been only a month since i joined graduate school and hoping to carry out research in crystallography.
I used ubuntu to install gromacs 3.3-1.5 using the synaptic and it worked like charm. I would however want the recent gromacs 3.3.3 version to be included in the repositories. That would be immensely beneficial.
Also, I have not been able to install the CCP4 crystallography suite of programs (www.ccp4.ac.uk) smoothly eventhough when I have all the dependent files installed. Is it possible that the ubuntu version be uploaded in the repositories. For example the ccp4mg, has some bugs when run in ubuntu.
it would be great if both the gromacs 3.3.3 and the ccp4 suite are tested in ubuntu and uploaded in the repos.
are there any crystallographers using ubuntu, that successfully installed the ccp4 suite (including the COOT package) ?.
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Last edited by nkamesh; March 3rd, 2008 at 06:13 AM..
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March 3rd, 2008 #2
LaserJock
Ubuntu Developer
Join Date: May 2005
Location: Reno,NV
Beans: 157
Ubuntu 8.10 Intrepid Ibex Re: crystallography and molecular dynamics packages in synaptic
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Quote:
Originally Posted by nkamesh
hi
I am a newbie to the linux world and recently installed ubuntu. Its been only a month since i joined graduate school and hoping to carry out research in crystallography.
I used ubuntu to install gromacs 3.3-1.5 using the synaptic and it worked like charm. I would however want the recent gromacs 3.3.3 version to be included in the repositories. That would be immensely beneficial.
Also, I have not been able to install the CCP4 crystallography suite of programs (www.ccp4.ac.uk) smoothly eventhough when I have all the dependent files installed. Is it possible that the ubuntu version be uploaded in the repositories. For example the ccp4mg, has some bugs when run in ubuntu.
it would be great if both the gromacs 3.3.3 and the ccp4 suite are tested in ubuntu and uploaded in the repos.
are there any crystallographers using ubuntu, that successfully installed the ccp4 suite (including the COOT package) ?.
Do you have any info on what specifically gromacs 3.3.3 would have over 3.3.2 which is what is scheduled to be released in Ubuntu 8.04? If we have a compelling reason we can file a Feature Freeze exception to try to get it in.
ccp4 is unfortunately not free enough to go into the usual Ubuntu repos. It probably would qualify for the Multiverse repo, which is used for non-free software, though.
-LaserJock
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March 3rd, 2008 #3
nkamesh
First Cup of Ubuntu
Join Date: Mar 2008
Beans: 2 Re: crystallography and molecular dynamics packages in synaptic
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There seem to be some issues with a small number of missing interactions between atoms when using a simulation box like the "rhombic dodecahedron"(http://www.gromacs.org/gromacs/revisions/)
I think its a commonly used simulation box and therefore would be important that the rectified features in the Gromacs be made available.
As for CCP4 suite - they are free set of programs for the crystallographic academic community and has some of the most versatile and most used packages. So they are definitely free for academic use. It would be great if it comes into the ubuntu repos after testing.
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Last edited by nkamesh; March 3rd, 2008 at 11:40 PM..
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March 4th, 2008 #4
Biochem
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Join Date: Feb 2007
Location: Montreal, Canada
Beans: 188
Ubuntu 8.04 Hardy Heron Re: crystallography and molecular dynamics packages in synaptic
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What Laserjock referer to with the word "free" is not only free of charge but also free to distribute and modify the software. In the case of CCP4 their licence stipulate:
1) Commercial organisations should contact us directly to arrange a licence.
2) The licence must be signed, and returned by fax or post (NOT email) to the following address:
So it is not free to modify and Canonical would probably have to call them to be sure that they have the right to distribute CCP4 in their repository. Also, the fact that you have your institution have to sign and fax the licence probably make it a bit complicated to put in the official repos.
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March 17th, 2009 #5
joshypyesudas
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Beans: 2 Re: crystallography and molecular dynamics packages in synaptic
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I installed Gromacs using Synaptic package manger in Ubuntu 8.10. But I dont know how to start and check whether Gromacs is installed. Could anyone please help me.
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