Dear Justin, Thanks for the options and suggestions, will be back after some trials with modelled proteins.
Ram On Mon, Sep 28, 2009 at 6:17 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > ram bio wrote: > >> Dear Justin, >> >> When I used the energy mininized system for NPT annealing with position >> restraints on lipids and there was no separation. So, I think I can proceed >> now to equiliration phase 2 (1-ns NPT equilibration-NPT) and then run the >> Molecular Dynamics for data collection(1ns).What do you suggest, is it the >> right way i am following..as i will be not be using NVT equillibration >> anywhere through out the process. >> >> > I think that should be fine. There is really no prescribed way to do > equilibration, necessarily. Everyone has their own method. If you can > stabilize the temperature and pressure prior to data collection, then you've > done enough, in general. Just be aware that my definition of "data > collection" simply means that you're remove restraints from anything that > was previously restrained. Collecting data for membrane protein systems > often occurs after 10-20 ns (or more), to allow for re-orientation of > lipids, which is very slow. > > -Justin > > Thanks, >> >> Ram >> >> >> On Fri, Sep 25, 2009 at 11:23 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> ram bio wrote: >> >> Dear Justin, >> >> As suggested, i increased the force constant in the Z dimension >> from 1000 to 10000, and did the NVT equillibration, but still >> the gap existed, then i gave the output of nvt equillibration >> that is nvt.gro as input for the NPT anneling simulation >> (suggested as with position constraints, 1000) and simulated and >> here also i had gap .between layers when npt.gro was viewed in VMD. >> >> I have a query that is can I use nvt equllibrated system as >> input for NPT simualated annealing or should I use the initial >> ionized and minimized system for the NPT annaelated simulation, >> as the gap is still persisting... >> >> >> Use the energy-minimized system as the input into annealing. I have >> no idea why this separation would be happening in this system, >> unless the box has been prepared improperly. I chose the KALP-DPPC >> system because it is very robust in everything we've tried to >> subject it to. >> >> -Justin >> >> Thanks >> >> Ram >> >> >> On Thu, Sep 24, 2009 at 4:16 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> ram bio wrote: >> >> Dear Justin, >> >> As suggested in the tutorial by you i applied the lipid >> position >> restraints, while running the NVT equillibration, but >> after the >> job is finished, when i observed the nvt.gro file in VMD, >> still >> there is a gap between the lipid bilayers but this time >> the gap >> is not so large as it was in the earlier run (as discussed >> earlier in previous email). >> >> As I was already running the NPT equillibration(which I >> obtained >> after the earlier NVT job, which ended in large gap between >> layers), i just wanted to observe it and here there is no >> gap in >> between the layers i.e. in npt.gro. >> >> Please suggest me what to do to lower the gap after NVT >> equillibration even after applying the lipid restraints >> and is >> it ok for my NPT equillibration as there are no gaps >> between the >> layers after this NPT equillibration. >> >> >> The gap arises because the lipids (when free to move) are >> attracted >> to the water above and below the bilayer. If the protein is >> restrained, it doesn't move. The box size in NVT is fixed, so >> the >> system is trying to fill it. It could be that your box was >> inappropriately assigned (too large), but maybe not. >> >> I am surprised that, even when using position restraints, the >> lipids >> still separated at all. Did you use the lipid_posre.itp file >> that I >> provide on the tutorial site? It has always worked well for >> me in >> such cases. You could also try increasing the force constant >> in the >> z-dimension. >> >> The other option is to do NPT simulated annealing, as I also >> suggest >> in the troubleshooting page. Using NPT allows the box to >> deform in >> response to the system, so you will probably get less weird >> behavior. I have found that both NVT with PR and simulated >> annealing can get the job done. >> >> -Justin >> >> Thanks >> >> Ram >> >> >> On Tue, Sep 22, 2009 at 8:25 PM, ram bio >> <rmbio...@gmail.com <mailto:rmbio...@gmail.com> >> <mailto:rmbio...@gmail.com <mailto:rmbio...@gmail.com>> >> <mailto:rmbio...@gmail.com <mailto:rmbio...@gmail.com> >> >> <mailto:rmbio...@gmail.com <mailto:rmbio...@gmail.com>>>> >> >> wrote: >> >> Dear Justin, >> >> Thanks for the suggestion, will try to apply position >> restraints on >> lipid as mentioned in the advanced trouble shooting >> section. >> >> Ram >> >> >> On Tue, Sep 22, 2009 at 8:08 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> wrote: >> >> >> >> ram bio wrote: >> >> Dear Gromacs Users, >> >> I am following the justin tutorial on KALP-15 >> in lipid >> bilayer, I have a query regarding the nvt.gro >> that is >> after >> the NVT equillibration phase. The mdrun was >> proper >> without >> any warnings or errors, but when i visuallized >> the >> nvt.gro >> in VMD, i found that the peptide is intact in >> between the >> bilayers, but the the two layers got separated or >> else it is >> like the peptide bridging the the two halves >> of the lipid >> bilayer with gap in between the layers and >> also found few >> water molecules to the sides of the peptide or >> in the gap >> mentioned betwwn the layers. >> >> Please let me know is the simulation going on >> normally or >> there is an defect or wrong going on, as the nvt >> equillibration was proper as i think i >> continued for the >> next equillibration that is npt for 1ns. >> >> >> You shouldn't continue blindly if you get weird >> results. >> Please >> see the "Advanced Troubleshooting" page (part of the >> tutorial!), >> because I specifically address the issue of a bilayer >> separating: >> >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/advanced_troubleshooting.html >> >> -Justin >> >> Ram >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list >> gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org >> >> >> <mailto:gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org>>> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/search >> before posting! >> Please don't post (un)subscribe requests to >> the list. Use >> the www interface or send it to >> gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>>. >> >> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> >> <http://vt.edu> | >> >> (540) 231-9080 >> >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org >> >> >> <mailto:gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org>>> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/search >> before posting! >> Please don't post (un)subscribe requests to the >> list. Use the >> www interface or send it to >> gmx-users-requ...@gromacs.org <mailto: >> gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>>. >> >> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) >> 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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