From: Tomasz M. <to...@bi...> - 2013-07-30 10:40:12
|
Dear PyMOL Users, I would like to announce you the plugin for PyMOL, which allows to perform molecular dynamics simulation on PyMOL loaded molecules using GROMACS and display results back to PyMOL in form of the animation. You can find more information on PyMOL Wiki: http://www.pymolwiki.org/index.php/GROMACS_Plugin and GitHub page of the project: https://github.com/tomaszmakarewicz/Dynamics The current work has been publish in scientific paper: http://pubs.acs.org/doi/abs/10.1021/ci400071x And you can find ready Ubuntu packages in following repository: https://launchpad.net/~tomaszm/+archive/dynamics If you have any question please do not hesitate to ask. In case of any bug, request or error please fill Issue on the GitHub page. Best regards, -- Tomasz Makarewicz, Laboratory of Biomolecular Systems Simulations, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Kładki 24, 80-822 Gdańsk, Poland ----------------------------------------- Ten list został wysłany z serwera Uniwersytetu Gdańskiego. http://www.ug.edu.pl/ |
From: Tomasz M. <to...@bi...> - 2013-08-01 07:37:03
|
Hi Thomas, Thanks for the report. Could you send me file "~/.dynamics/NameOfMolecule/log.txt". It contains every GROMACS output, so we will be able to analyse, what exactly GROMACS is missing. You should also not remove those two lines of code. This is the part of code, which in case of such an error analyse "log.txt" file and create window on the screen, which contain useful information. Best regards, -- Tomasz Makarewicz, Laboratory of Biomolecular Systems Simulations, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Kładki 24, 80-822 Gdańsk, Poland > Hi Tomasz, > > I quickly tested your plugin but wasn't able to run a similation. I have > gromacs 4.6.2 on Linux. This is what I got: > > Starting PyMOL plugin 'dynamics' ver. 2.0.0pre by Tomasz Makarewicz > updating project files > Calculating topology using Force fields > updating project files > Generating waterbox > Adding Water Box > updating project files > Energy Minimization > Unable to perform Energy Minimization > Fatal error: > There was 1 error in input file(s) > For more information and tips for troubleshooting, please check the > GROMACS > website at http://www.gromacs.org/Documentation/Errors > > Also on line 1078, I replaced Tk() by Toplevel() and dropped > root.mainloop() on line 1086 because that gave an error. > > Cheers, > Thomas > > Tomasz Makarewicz wrote, On 07/30/13 12:19: >> Dear PyMOL Users, >> >> I would like to announce you the plugin for PyMOL, which allows to >> perform >> molecular dynamics simulation on PyMOL loaded molecules using GROMACS >> and >> display results back to PyMOL in form of the animation. >> You can find more information on PyMOL Wiki: >> http://www.pymolwiki.org/index.php/GROMACS_Plugin >> and GitHub page of the project: >> https://github.com/tomaszmakarewicz/Dynamics >> The current work has been publish in scientific paper: >> http://pubs.acs.org/doi/abs/10.1021/ci400071x >> And you can find ready Ubuntu packages in following repository: >> https://launchpad.net/~tomaszm/+archive/dynamics >> >> If you have any question please do not hesitate to ask. >> >> In case of any bug, request or error please fill Issue on the GitHub >> page. >> >> Best regards, > > -- > Thomas Holder > PyMOL Developer > Schrödinger Contractor ----------------------------------------- Ten list został wysłany z serwera Uniwersytetu Gdańskiego. http://www.ug.edu.pl/ |
From: Thomas H. <tho...@sc...> - 2013-08-01 07:57:01
|
Hi Tomasz, Tomasz Makarewicz wrote, On 08/01/13 09:36: > Thanks for the report. Could you send me file > "~/.dynamics/NameOfMolecule/log.txt". It contains every GROMACS output, so > we will be able to analyse, what exactly GROMACS is missing. The relevant error seems to be: ERROR 1 [file foo.top, line 710]: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. Full log: http://pymol.org/tmp/dynamics-log.txt Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger Contractor |
From: Tomasz M. <to...@bi...> - 2013-08-01 08:09:07
|
Hi Thomas, That's pretty easy. Water-box is just too small. You can increase the water-box size by pressing "Configure" in the main plugin window under the "Water Model" label. Best regards, -- Tomasz Makarewicz, Laboratory of Biomolecular Systems Simulations, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Kładki 24, 80-822 Gdańsk, Poland > Hi Tomasz, > > Tomasz Makarewicz wrote, On 08/01/13 09:36: >> Thanks for the report. Could you send me file >> "~/.dynamics/NameOfMolecule/log.txt". It contains every GROMACS output, >> so >> we will be able to analyse, what exactly GROMACS is missing. > > The relevant error seems to be: > > ERROR 1 [file foo.top, line 710]: > ERROR: The cut-off length is longer than half the shortest box vector > or longer than the smallest box diagonal element. Increase the box > size or decrease rlist. > > Full log: > http://pymol.org/tmp/dynamics-log.txt > > Cheers, > Thomas > > -- > Thomas Holder > PyMOL Developer > Schrödinger Contractor > > ------------------------------------------------------------------------------ > Get your SQL database under version control now! > Version control is standard for application code, but databases havent > caught up. So what steps can you take to put your SQL databases under > version control? Why should you start doing it? Read more to find out. > http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... ----------------------------------------- Ten list został wysłany z serwera Uniwersytetu Gdańskiego. http://www.ug.edu.pl/ |
From: Tsjerk W. <ts...@gm...> - 2013-08-01 08:06:45
|
Hey :) I guess you tried the plugin with something quite small, using a too small distance between periodic images. This should be caught off by a check in the plugin, resetting the simulation cell if the usual criteria result in a too small one. The best way, IMHO, is checking the last line of the .gro file obtained with editconf and replacing it by a 3.0 nm rhombic dodecahedron or cube. Not sure what the default box type is, but it should be a rhombic dodecahedron :) I notice from the log that a rectangular cell was used. Cheers, Tsjerk On Thu, Aug 1, 2013 at 9:56 AM, Thomas Holder <tho...@sc... > wrote: > Hi Tomasz, > > Tomasz Makarewicz wrote, On 08/01/13 09:36: > > Thanks for the report. Could you send me file > > "~/.dynamics/NameOfMolecule/log.txt". It contains every GROMACS output, > so > > we will be able to analyse, what exactly GROMACS is missing. > > The relevant error seems to be: > > ERROR 1 [file foo.top, line 710]: > ERROR: The cut-off length is longer than half the shortest box vector > or longer than the smallest box diagonal element. Increase the box > size or decrease rlist. > > Full log: > http://pymol.org/tmp/dynamics-log.txt > > Cheers, > Thomas > > -- > Thomas Holder > PyMOL Developer > Schrödinger Contractor > > > ------------------------------------------------------------------------------ > Get your SQL database under version control now! > Version control is standard for application code, but databases havent > caught up. So what steps can you take to put your SQL databases under > version control? Why should you start doing it? Read more to find out. > http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Tsjerk A. Wassenaar, Ph.D. |
From: Tomasz M. <to...@bi...> - 2013-08-01 08:18:39
|
Hi Tsjerk, Both size and shape of waterbox can be choose by GUI via plugin, by clicking "Configure" under "Water Model" label in main plugin window. Anyway, thanks for the tip. Best regards, -- Tomasz Makarewicz, Laboratory of Biomolecular Systems Simulations, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Kładki 24, 80-822 Gdańsk, Poland > Hey :) > > I guess you tried the plugin with something quite small, using a too small > distance between periodic images. This should be caught off by a check in > the plugin, resetting the simulation cell if the usual criteria result in > a > too small one. The best way, IMHO, is checking the last line of the .gro > file obtained with editconf and replacing it by a 3.0 nm rhombic > dodecahedron or cube. Not sure what the default box type is, but it should > be a rhombic dodecahedron :) I notice from the log that a rectangular cell > was used. > > Cheers, > > Tsjerk > > > On Thu, Aug 1, 2013 at 9:56 AM, Thomas Holder > <tho...@sc... >> wrote: > >> Hi Tomasz, >> >> Tomasz Makarewicz wrote, On 08/01/13 09:36: >> > Thanks for the report. Could you send me file >> > "~/.dynamics/NameOfMolecule/log.txt". It contains every GROMACS >> output, >> so >> > we will be able to analyse, what exactly GROMACS is missing. >> >> The relevant error seems to be: >> >> ERROR 1 [file foo.top, line 710]: >> ERROR: The cut-off length is longer than half the shortest box vector >> or longer than the smallest box diagonal element. Increase the box >> size or decrease rlist. >> >> Full log: >> http://pymol.org/tmp/dynamics-log.txt >> >> Cheers, >> Thomas >> >> -- >> Thomas Holder >> PyMOL Developer >> Schrödinger Contractor >> >> >> ------------------------------------------------------------------------------ >> Get your SQL database under version control now! >> Version control is standard for application code, but databases havent >> caught up. So what steps can you take to put your SQL databases under >> version control? Why should you start doing it? Read more to find out. >> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > ------------------------------------------------------------------------------ > Get your SQL database under version control now! > Version control is standard for application code, but databases havent > caught up. So what steps can you take to put your SQL databases under > version control? Why should you start doing it? Read more to find out. > http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk_______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... ----------------------------------------- Ten list został wysłany z serwera Uniwersytetu Gdańskiego. http://www.ug.edu.pl/ |
From: Tsjerk W. <ts...@gm...> - 2013-08-01 08:24:15
|
Hi Tomasz, Sure, the user can do it all, but the plugin is meant to take trouble away from the user. Now you let the user run into some error, which does not give a good hint how to solve the issue. If there is a standard solution, which here is setting the box to some minimum allowable size, the plugin should take care of it. The other point is about defaults, I would have guessed the user can specify the box type, but the plugin, by default, should suggest the optimal one, which is a rhombic dodecahedron. Nice work though! :) Cheers, Tsjerk On Thu, Aug 1, 2013 at 10:18 AM, Tomasz Makarewicz < to...@bi...> wrote: > Hi Tsjerk, > > Both size and shape of waterbox can be choose by GUI via plugin, by > clicking "Configure" under "Water Model" label in main plugin window. > Anyway, thanks for the tip. > > Best regards, > -- > Tomasz Makarewicz, > Laboratory of Biomolecular Systems Simulations, > Intercollegiate Faculty of Biotechnology, > University of Gdańsk and Medical University of Gdańsk, > Kładki 24, 80-822 Gdańsk, Poland > > > > Hey :) > > > > I guess you tried the plugin with something quite small, using a too > small > > distance between periodic images. This should be caught off by a check in > > the plugin, resetting the simulation cell if the usual criteria result in > > a > > too small one. The best way, IMHO, is checking the last line of the .gro > > file obtained with editconf and replacing it by a 3.0 nm rhombic > > dodecahedron or cube. Not sure what the default box type is, but it > should > > be a rhombic dodecahedron :) I notice from the log that a rectangular > cell > > was used. > > > > Cheers, > > > > Tsjerk > > > > > > On Thu, Aug 1, 2013 at 9:56 AM, Thomas Holder > > <tho...@sc... > >> wrote: > > > >> Hi Tomasz, > >> > >> Tomasz Makarewicz wrote, On 08/01/13 09:36: > >> > Thanks for the report. Could you send me file > >> > "~/.dynamics/NameOfMolecule/log.txt". It contains every GROMACS > >> output, > >> so > >> > we will be able to analyse, what exactly GROMACS is missing. > >> > >> The relevant error seems to be: > >> > >> ERROR 1 [file foo.top, line 710]: > >> ERROR: The cut-off length is longer than half the shortest box vector > >> or longer than the smallest box diagonal element. Increase the box > >> size or decrease rlist. > >> > >> Full log: > >> http://pymol.org/tmp/dynamics-log.txt > >> > >> Cheers, > >> Thomas > >> > >> -- > >> Thomas Holder > >> PyMOL Developer > >> Schrödinger Contractor > >> > >> > >> > ------------------------------------------------------------------------------ > >> Get your SQL database under version control now! > >> Version control is standard for application code, but databases havent > >> caught up. So what steps can you take to put your SQL databases under > >> version control? Why should you start doing it? Read more to find out. > >> > http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk > >> _______________________________________________ > >> PyMOL-users mailing list (PyM...@li...) > >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > >> Archives: http://www.mail-archive.com/pym...@li... > >> > > > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > > ------------------------------------------------------------------------------ > > Get your SQL database under version control now! > > Version control is standard for application code, but databases havent > > caught up. So what steps can you take to put your SQL databases under > > version control? Why should you start doing it? Read more to find out. > > > http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk_______________________________________________ > > PyMOL-users mailing list (PyM...@li...) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pym...@li... > > > ----------------------------------------- > Ten list został wysłany z serwera Uniwersytetu Gdańskiego. > http://www.ug.edu.pl/ > > -- Tsjerk A. Wassenaar, Ph.D. |
From: Tomasz M. <to...@bi...> - 2013-08-01 08:34:11
|
Hi Tsjerk, It is not so easy to please all. If fact molecular dynamics simulation is so complex matter, that most setting should be set case by case. Plugin manual describe how to deal with different options. As it goes to waterbox, plugin is using default GROMACS options. Default size is relative to molecule size and should work for most cases. The reason, why I did not increase it more by default, is that size of waterbox is most important factor for calculation time. A little bigger waterbox, increase calculation time drastically. Best regards, -- Tomasz Makarewicz, Laboratory of Biomolecular Systems Simulations, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Kładki 24, 80-822 Gdańsk, Poland > Hi Tomasz, > > Sure, the user can do it all, but the plugin is meant to take trouble away > from the user. Now you let the user run into some error, which does not > give a good hint how to solve the issue. If there is a standard solution, > which here is setting the box to some minimum allowable size, the plugin > should take care of it. The other point is about defaults, I would have > guessed the user can specify the box type, but the plugin, by default, > should suggest the optimal one, which is a rhombic dodecahedron. > > Nice work though! :) > > Cheers, > > Tsjerk > > > > On Thu, Aug 1, 2013 at 10:18 AM, Tomasz Makarewicz < > to...@bi...> wrote: > >> Hi Tsjerk, >> >> Both size and shape of waterbox can be choose by GUI via plugin, by >> clicking "Configure" under "Water Model" label in main plugin window. >> Anyway, thanks for the tip. >> >> Best regards, >> -- >> Tomasz Makarewicz, >> Laboratory of Biomolecular Systems Simulations, >> Intercollegiate Faculty of Biotechnology, >> University of Gdańsk and Medical University of Gdańsk, >> Kładki 24, 80-822 Gdańsk, Poland >> >> >> > Hey :) >> > >> > I guess you tried the plugin with something quite small, using a too >> small >> > distance between periodic images. This should be caught off by a check >> in >> > the plugin, resetting the simulation cell if the usual criteria result >> in >> > a >> > too small one. The best way, IMHO, is checking the last line of the >> .gro >> > file obtained with editconf and replacing it by a 3.0 nm rhombic >> > dodecahedron or cube. Not sure what the default box type is, but it >> should >> > be a rhombic dodecahedron :) I notice from the log that a rectangular >> cell >> > was used. >> > >> > Cheers, >> > >> > Tsjerk >> > >> > >> > On Thu, Aug 1, 2013 at 9:56 AM, Thomas Holder >> > <tho...@sc... >> >> wrote: >> > >> >> Hi Tomasz, >> >> >> >> Tomasz Makarewicz wrote, On 08/01/13 09:36: >> >> > Thanks for the report. Could you send me file >> >> > "~/.dynamics/NameOfMolecule/log.txt". It contains every GROMACS >> >> output, >> >> so >> >> > we will be able to analyse, what exactly GROMACS is missing. >> >> >> >> The relevant error seems to be: >> >> >> >> ERROR 1 [file foo.top, line 710]: >> >> ERROR: The cut-off length is longer than half the shortest box >> vector >> >> or longer than the smallest box diagonal element. Increase the box >> >> size or decrease rlist. >> >> >> >> Full log: >> >> http://pymol.org/tmp/dynamics-log.txt >> >> >> >> Cheers, >> >> Thomas >> >> >> >> -- >> >> Thomas Holder >> >> PyMOL Developer >> >> Schrödinger Contractor >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> Get your SQL database under version control now! >> >> Version control is standard for application code, but databases >> havent >> >> caught up. So what steps can you take to put your SQL databases under >> >> version control? Why should you start doing it? Read more to find >> out. >> >> >> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk >> >> _______________________________________________ >> >> PyMOL-users mailing list (PyM...@li...) >> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> Archives: >> http://www.mail-archive.com/pym...@li... >> >> >> > >> > >> > >> > -- >> > Tsjerk A. Wassenaar, Ph.D. >> > >> ------------------------------------------------------------------------------ >> > Get your SQL database under version control now! >> > Version control is standard for application code, but databases havent >> > caught up. So what steps can you take to put your SQL databases under >> > version control? Why should you start doing it? Read more to find out. >> > >> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk_______________________________________________ >> > PyMOL-users mailing list (PyM...@li...) >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> > Archives: >> http://www.mail-archive.com/pym...@li... >> >> >> ----------------------------------------- >> Ten list został wysłany z serwera Uniwersytetu Gdańskiego. >> http://www.ug.edu.pl/ >> >> > > > -- > Tsjerk A. Wassenaar, Ph.D. ----------------------------------------- Ten list został wysłany z serwera Uniwersytetu Gdańskiego. http://www.ug.edu.pl/ |
From: Tsjerk W. <ts...@gm...> - 2013-08-01 09:24:11
|
Hi Tomasz, I think you don't need to explain to me how complex MD is :) My assumption is that your plugin is aimed primarily at simulations of a protein or so in solution, and cares to facilitate that. So, that sets the case. The main choice the user has is about the force field. That then determines most of the settings, as the electrostatics, etc, are essentially part of the force field. For the box, a rectangular unit cell is problematic if the solute rotates, so you shouldn't use that, even if it is the default. If the choice is then between a cubic and a rhombic dodecahedron, the latter is 71% of the size of the former, for whichever distance between images, so it will always be more efficient. The default size depends on what you put in. Thomas tried it on a heptapeptide, and it didn't work. In fact, as it is now, it wil only work out of the box for larger solutes. If you set a lower bound for the box size, it will also work for anything small. Out of curiosity, as I still have to try the plugin, how do you deal with alternative protonation states? Can you set them by clicking on the sequence? :) Cheers, Tsjerk On Thu, Aug 1, 2013 at 10:33 AM, Tomasz Makarewicz < to...@bi...> wrote: > Hi Tsjerk, > > It is not so easy to please all. If fact molecular dynamics simulation is > so complex matter, that most setting should be set case by case. Plugin > manual describe how to deal with different options. As it goes to > waterbox, plugin is using default GROMACS options. Default size is > relative to molecule size and should work for most cases. The reason, why > I did not increase it more by default, is that size of waterbox is most > important factor for calculation time. A little bigger waterbox, increase > calculation time drastically. > > Best regards, > -- > Tomasz Makarewicz, > Laboratory of Biomolecular Systems Simulations, > Intercollegiate Faculty of Biotechnology, > University of Gdańsk and Medical University of Gdańsk, > Kładki 24, 80-822 Gdańsk, Poland > > > Hi Tomasz, > > > > Sure, the user can do it all, but the plugin is meant to take trouble > away > > from the user. Now you let the user run into some error, which does not > > give a good hint how to solve the issue. If there is a standard solution, > > which here is setting the box to some minimum allowable size, the plugin > > should take care of it. The other point is about defaults, I would have > > guessed the user can specify the box type, but the plugin, by default, > > should suggest the optimal one, which is a rhombic dodecahedron. > > > > Nice work though! :) > > > > Cheers, > > > > Tsjerk > > > > > > > > On Thu, Aug 1, 2013 at 10:18 AM, Tomasz Makarewicz < > > to...@bi...> wrote: > > > >> Hi Tsjerk, > >> > >> Both size and shape of waterbox can be choose by GUI via plugin, by > >> clicking "Configure" under "Water Model" label in main plugin window. > >> Anyway, thanks for the tip. > >> > >> Best regards, > >> -- > >> Tomasz Makarewicz, > >> Laboratory of Biomolecular Systems Simulations, > >> Intercollegiate Faculty of Biotechnology, > >> University of Gdańsk and Medical University of Gdańsk, > >> Kładki 24, 80-822 Gdańsk, Poland > >> > >> > >> > Hey :) > >> > > >> > I guess you tried the plugin with something quite small, using a too > >> small > >> > distance between periodic images. This should be caught off by a check > >> in > >> > the plugin, resetting the simulation cell if the usual criteria result > >> in > >> > a > >> > too small one. The best way, IMHO, is checking the last line of the > >> .gro > >> > file obtained with editconf and replacing it by a 3.0 nm rhombic > >> > dodecahedron or cube. Not sure what the default box type is, but it > >> should > >> > be a rhombic dodecahedron :) I notice from the log that a rectangular > >> cell > >> > was used. > >> > > >> > Cheers, > >> > > >> > Tsjerk > >> > > >> > > >> > On Thu, Aug 1, 2013 at 9:56 AM, Thomas Holder > >> > <tho...@sc... > >> >> wrote: > >> > > >> >> Hi Tomasz, > >> >> > >> >> Tomasz Makarewicz wrote, On 08/01/13 09:36: > >> >> > Thanks for the report. Could you send me file > >> >> > "~/.dynamics/NameOfMolecule/log.txt". It contains every GROMACS > >> >> output, > >> >> so > >> >> > we will be able to analyse, what exactly GROMACS is missing. > >> >> > >> >> The relevant error seems to be: > >> >> > >> >> ERROR 1 [file foo.top, line 710]: > >> >> ERROR: The cut-off length is longer than half the shortest box > >> vector > >> >> or longer than the smallest box diagonal element. Increase the box > >> >> size or decrease rlist. > >> >> > >> >> Full log: > >> >> http://pymol.org/tmp/dynamics-log.txt > >> >> > >> >> Cheers, > >> >> Thomas > >> >> > >> >> -- > >> >> Thomas Holder > >> >> PyMOL Developer > >> >> Schrödinger Contractor > >> >> > >> >> > >> >> > >> > ------------------------------------------------------------------------------ > >> >> Get your SQL database under version control now! > >> >> Version control is standard for application code, but databases > >> havent > >> >> caught up. So what steps can you take to put your SQL databases under > >> >> version control? Why should you start doing it? Read more to find > >> out. > >> >> > >> > http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk > >> >> _______________________________________________ > >> >> PyMOL-users mailing list (PyM...@li...) > >> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > >> >> Archives: > >> http://www.mail-archive.com/pym...@li... > >> >> > >> > > >> > > >> > > >> > -- > >> > Tsjerk A. Wassenaar, Ph.D. > >> > > >> > ------------------------------------------------------------------------------ > >> > Get your SQL database under version control now! > >> > Version control is standard for application code, but databases havent > >> > caught up. So what steps can you take to put your SQL databases under > >> > version control? Why should you start doing it? Read more to find out. > >> > > >> > http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk_______________________________________________ > >> > PyMOL-users mailing list (PyM...@li...) > >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > >> > Archives: > >> http://www.mail-archive.com/pym...@li... > >> > >> > >> ----------------------------------------- > >> Ten list został wysłany z serwera Uniwersytetu Gdańskiego. > >> http://www.ug.edu.pl/ > >> > >> > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > > ----------------------------------------- > Ten list został wysłany z serwera Uniwersytetu Gdańskiego. > http://www.ug.edu.pl/ > > -- Tsjerk A. Wassenaar, Ph.D. |
From: Tomasz M. <to...@bi...> - 2013-08-01 11:37:08
|
Hi Tsjerk, Thank you for the tips about water-box. I have opened new issue and after some verification I will most probably include it by default: https://github.com/tomaszmakarewicz/Dynamics/issues/48 As it goes to "alternative protonation states", well GROMACS is big and many of its functionalities are not yet implemented. At the moment pdb2gmx adds protons to the molecule as it wants. There is now way to influence it directly or indirectly (via pH) by the plugin. If you see this functionality as an essential, please fill the issue on project GitHub page: https://github.com/tomaszmakarewicz/Dynamics/issues?state=open I would also appreciate if together with issue, you will provide reference GROMACS method of handling it. As far as I know, even GROMACS developers are still scratching their heads, how to implement this: http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation Best regards, -- Tomasz Makarewicz, Laboratory of Biomolecular Systems Simulations, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Kładki 24, 80-822 Gdańsk, Poland > Hi Tomasz, > > I think you don't need to explain to me how complex MD is :) > My assumption is that your plugin is aimed primarily at simulations of a > protein or so in solution, and cares to facilitate that. So, that sets the > case. The main choice the user has is about the force field. That then > determines most of the settings, as the electrostatics, etc, are > essentially part of the force field. For the box, a rectangular unit cell > is problematic if the solute rotates, so you shouldn't use that, even if > it > is the default. If the choice is then between a cubic and a rhombic > dodecahedron, the latter is 71% of the size of the former, for whichever > distance between images, so it will always be more efficient. The default > size depends on what you put in. Thomas tried it on a heptapeptide, and it > didn't work. In fact, as it is now, it wil only work out of the box for > larger solutes. If you set a lower bound for the box size, it will also > work for anything small. > > Out of curiosity, as I still have to try the plugin, how do you deal with > alternative protonation states? Can you set them by clicking on the > sequence? :) > > Cheers, > > Tsjerk > > > > On Thu, Aug 1, 2013 at 10:33 AM, Tomasz Makarewicz < > to...@bi...> wrote: > >> Hi Tsjerk, >> >> It is not so easy to please all. If fact molecular dynamics simulation >> is >> so complex matter, that most setting should be set case by case. Plugin >> manual describe how to deal with different options. As it goes to >> waterbox, plugin is using default GROMACS options. Default size is >> relative to molecule size and should work for most cases. The reason, >> why >> I did not increase it more by default, is that size of waterbox is most >> important factor for calculation time. A little bigger waterbox, >> increase >> calculation time drastically. >> >> Best regards, >> -- >> Tomasz Makarewicz, >> Laboratory of Biomolecular Systems Simulations, >> Intercollegiate Faculty of Biotechnology, >> University of Gdańsk and Medical University of Gdańsk, >> Kładki 24, 80-822 Gdańsk, Poland >> >> > Hi Tomasz, >> > >> > Sure, the user can do it all, but the plugin is meant to take trouble >> away >> > from the user. Now you let the user run into some error, which does >> not >> > give a good hint how to solve the issue. If there is a standard >> solution, >> > which here is setting the box to some minimum allowable size, the >> plugin >> > should take care of it. The other point is about defaults, I would >> have >> > guessed the user can specify the box type, but the plugin, by default, >> > should suggest the optimal one, which is a rhombic dodecahedron. >> > >> > Nice work though! :) >> > >> > Cheers, >> > >> > Tsjerk >> > >> > >> > >> > On Thu, Aug 1, 2013 at 10:18 AM, Tomasz Makarewicz < >> > to...@bi...> wrote: >> > >> >> Hi Tsjerk, >> >> >> >> Both size and shape of waterbox can be choose by GUI via plugin, by >> >> clicking "Configure" under "Water Model" label in main plugin window. >> >> Anyway, thanks for the tip. >> >> >> >> Best regards, >> >> -- >> >> Tomasz Makarewicz, >> >> Laboratory of Biomolecular Systems Simulations, >> >> Intercollegiate Faculty of Biotechnology, >> >> University of Gdańsk and Medical University of Gdańsk, >> >> Kładki 24, 80-822 Gdańsk, Poland >> >> >> >> >> >> > Hey :) >> >> > >> >> > I guess you tried the plugin with something quite small, using a >> too >> >> small >> >> > distance between periodic images. This should be caught off by a >> check >> >> in >> >> > the plugin, resetting the simulation cell if the usual criteria >> result >> >> in >> >> > a >> >> > too small one. The best way, IMHO, is checking the last line of the >> >> .gro >> >> > file obtained with editconf and replacing it by a 3.0 nm rhombic >> >> > dodecahedron or cube. Not sure what the default box type is, but it >> >> should >> >> > be a rhombic dodecahedron :) I notice from the log that a >> rectangular >> >> cell >> >> > was used. >> >> > >> >> > Cheers, >> >> > >> >> > Tsjerk >> >> > >> >> > >> >> > On Thu, Aug 1, 2013 at 9:56 AM, Thomas Holder >> >> > <tho...@sc... >> >> >> wrote: >> >> > >> >> >> Hi Tomasz, >> >> >> >> >> >> Tomasz Makarewicz wrote, On 08/01/13 09:36: >> >> >> > Thanks for the report. Could you send me file >> >> >> > "~/.dynamics/NameOfMolecule/log.txt". It contains every GROMACS >> >> >> output, >> >> >> so >> >> >> > we will be able to analyse, what exactly GROMACS is missing. >> >> >> >> >> >> The relevant error seems to be: >> >> >> >> >> >> ERROR 1 [file foo.top, line 710]: >> >> >> ERROR: The cut-off length is longer than half the shortest box >> >> vector >> >> >> or longer than the smallest box diagonal element. Increase the >> box >> >> >> size or decrease rlist. >> >> >> >> >> >> Full log: >> >> >> http://pymol.org/tmp/dynamics-log.txt >> >> >> >> >> >> Cheers, >> >> >> Thomas >> >> >> >> >> >> -- >> >> >> Thomas Holder >> >> >> PyMOL Developer >> >> >> Schrödinger Contractor >> >> >> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> >> Get your SQL database under version control now! >> >> >> Version control is standard for application code, but databases >> >> havent >> >> >> caught up. So what steps can you take to put your SQL databases >> under >> >> >> version control? Why should you start doing it? Read more to find >> >> out. >> >> >> >> >> >> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk >> >> >> _______________________________________________ >> >> >> PyMOL-users mailing list (PyM...@li...) >> >> >> Info Page: >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> >> Archives: >> >> http://www.mail-archive.com/pym...@li... >> >> >> >> >> > >> >> > >> >> > >> >> > -- >> >> > Tsjerk A. Wassenaar, Ph.D. >> >> > >> >> >> ------------------------------------------------------------------------------ >> >> > Get your SQL database under version control now! >> >> > Version control is standard for application code, but databases >> havent >> >> > caught up. So what steps can you take to put your SQL databases >> under >> >> > version control? Why should you start doing it? Read more to find >> out. >> >> > >> >> >> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk_______________________________________________ >> >> > PyMOL-users mailing list (PyM...@li...) >> >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> > Archives: >> >> http://www.mail-archive.com/pym...@li... >> >> >> >> >> >> ----------------------------------------- >> >> Ten list został wysłany z serwera Uniwersytetu Gdańskiego. >> >> http://www.ug.edu.pl/ >> >> >> >> >> > >> > >> > -- >> > Tsjerk A. Wassenaar, Ph.D. >> >> >> ----------------------------------------- >> Ten list został wysłany z serwera Uniwersytetu Gdańskiego. >> http://www.ug.edu.pl/ >> >> > > > -- > Tsjerk A. Wassenaar, Ph.D. ----------------------------------------- Ten list został wysłany z serwera Uniwersytetu Gdańskiego. http://www.ug.edu.pl/ |