Re: [gmx-users] Merry Christmas from MemProtMD
Dear Tom, Thanks for the poem, the fantastic job on membrane proteins! Merry Christmas and happy New Year Best, Stéphane Le 25/12/2016 à 21:53, Tom Newport a écrit : *With apologies to Clement Clarke Moore* 1. Twas the night before Christmas, when all through the PDB, Not a protein was stirring, not even TatC, The ligands were bound in their structures with care, Hoping coarse-grained parameters soon would be there. 2. The tired crystal structures settled down for their naps, all snugly fitted to electron density maps. Then suddenly Santa, with all the strength he could muster, Burst into the scene with a GPU cluster. 3. He said with a smile: It’s simply not right; Membrane proteins should move on this most festive night. I’ll bring them to life, using MemProtMD, Run martinize, then add DPPC. 4. He promised them wonders, full of joy, full of fun, as he typed into bash $ gmx mdrun. The magic had started; they cheered and they jumped. And then on the screen: Error. Seg Fault. Core Dumped. 5. I’m sure we can fix this, he says as he winks, Now what is this error - something about lincs? He checked his coordinates, then checked all the files, That once jolly face had lost all its smiles. 6. He recompiled the kernel, reconfigured libcuda, As the words he was using grew steadily ruder. Through tears of frustration, he could barely persist, Even braved the wrath of the gromacs mailing list. 7. But before he stomped off to the pub down the road, He saw in a thread “reboot the headnode”, And quick as a flash, but quite unexplained, The jobs were all running, correctly constrained. 8. Santa, it seems, was jolly once more, Asked the kids to forget all those words from before. As each job completed, he chuckled with glee, Then converted to GROMOS with CG2AT 9. He used libraries in Python to run though trajectories, And added analyses to the simulations’ directories. Built database indexes and sent it all back, To some docker containers on a decade old mac. 10. The web application at last was deployed, And each membrane protein was quite overjoyed. Annotated and ready, to the web-app they came, And with metadata he could call them by name. 11. There’s OmpF, there’s TatC and GPCRs, Ionotropic receptors and domains we call BARs. A few aquaporins, a receptor for glycine, And LSPA, with bound globomycin. 12. And once he was done, folks near or far, Could find simulations with just a search bar. Then once a suitable protein was found, See all the sites where a lipid had bound. 13. Download the data, add in some ligands, Modify the membrane and see if it thickened. Run new simulations, see what patterns emerged, Then run it twice more and pretend it converged. 14. My work here is done, Santa said with a grin, I’m off to the pub to get plastered on gin. May all your experiments turn out alright; Merry Christmas to all, and to all a good night. -- Lecturer, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Continuing a FEP alchemical
Hello Gromacs user, I have a free energy simulation converged results harvested by alchemcial analysis in 15 lambada windows, now, I would like to increase the number of lambada windows to 20. Would you please let me know how I can continue my old simulation with 15 windows to 20 windows? Regards, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Continuing a FEP alchemical
On Wed, 28 Dec 2016 16:40:49 +0100 Alex wrote: > Hello Gromacs user, > > I have a free energy simulation converged results harvested by > alchemcial analysis in 15 lambada windows, now, I would like to > increase the number of lambada windows to 20. Would you please let me > know how I can continue my old simulation with 15 windows to 20 > windows? Just add the additional lambda points to your lambda vector and run the simulations for those. For TI analysis this is all you need to do. For FEP style analysis you would need to make sure that you also have the energy projections for the neighbouring lambda(s). You should be able to use the -rerun feature to compute those (but think about nstxout != nstdhdl). -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Continuing a FEP alchemical
Thank for your response. You mean for the TI analysis, now problem if one .xvg file (e.g. case.3.xvg) has just 15 columns while another .xvg file (e.g. case.18.xvg) has 20 columns? and still the "alchemical analysis package" could be used to calculate the free energy change via TI method? Thanks Regards, Alex On Wed, Dec 28, 2016 at 5:12 PM, Hannes Loeffler wrote: > On Wed, 28 Dec 2016 16:40:49 +0100 > Alex wrote: > > > Hello Gromacs user, > > > > I have a free energy simulation converged results harvested by > > alchemcial analysis in 15 lambada windows, now, I would like to > > increase the number of lambada windows to 20. Would you please let me > > know how I can continue my old simulation with 15 windows to 20 > > windows? > > Just add the additional lambda points to your lambda vector and run > the simulations for those. For TI analysis this is all you need to do. > For FEP style analysis you would need to make sure that you also have > the energy projections for the neighbouring lambda(s). You should be > able to use the -rerun feature to compute those (but think about > nstxout != nstdhdl). > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Continuing a FEP alchemical
On Wed, 28 Dec 2016 17:24:08 +0100 Alex wrote: > Thank for your response. > > You mean for the TI analysis, now problem if one .xvg file (e.g. > case.3.xvg) has just 15 columns while another .xvg file (e.g. > case.18.xvg) has 20 columns? and still the "alchemical analysis > package" could be used to calculate the free energy change via TI > method? I suppose you mean David Mobley's tool. Yes, it can do that. You can easily check that yourself though. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] ffnonbonded.itp
Hi If some can send me the modified ffnonbonded.itp and lipid.itp used for gromacs membrane tutorial. Some how I deleted more then whats necessary and would like to compare what needs to keep and what needs modification. best J. Vitali -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Reading tpx file (md_0_1.tpr) version 110 with version 100 program
Dear Gromacs, I use "gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr" to generate the tpr file on my own PC. Then I submitted it to our university computer cluster, in which an older version is installed, and I got the Fatal error: Reading tpx file (md_0_1.tpr) version 110 with version 100 program I know I should use the same old version to generate the tpr file. But should I unstall the newer one, and install the older one? Can I use the newer Gromacs to generate the old tpr file? Thank you. Yours sincerely Cheng -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Reading tpx file (md_0_1.tpr) version 110 with version 100 program
Newer. Always newer! On Wed, Dec 28, 2016 at 2:11 PM, Zhang, Cheng wrote: > Dear Gromacs, > > I use "gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o > md_0_1.tpr" to generate the tpr file on my own PC. Then I submitted it to > our university computer cluster, in which an older version is installed, > and I got the Fatal error: > > > Reading tpx file (md_0_1.tpr) version 110 with version 100 program > > > I know I should use the same old version to generate the tpr file. But > should I unstall the newer one, and install the older one? > > > Can I use the newer Gromacs to generate the old tpr file? Thank you. > > > Yours sincerely > > Cheng > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] New inGromacs
Hi every one. am new with Gromacs, for going to 4 months now. i have been working through the online tutorials to get some of the commands of Gramacs. i see different conferences and seminars being organized in different parts europe. am from Nigeria and stay here in nigeria, butno conference/seminar has been organized here in nigeria is the Gromacs Administrators not interested in developing the software around african countries?. i really want to know the Gromacs in details -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
