Thank you for the tip. I will try to use it. Amit On Fri, Oct 9, 2009 at 6:10 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Amit Choubey wrote: > >> Hi Justin, >> >> Yes you are right. I didnt fix the periodicity to start with. Could you >> tell me how to do that, which command to work with? >> Thanks. >> >> > Periodicity is corrected using trjconv. This involves creating a .tpr file > of to represent the system and using trjconv -pbc mol -ur compact, or some > such equivalent. > > My tutorial gives some information on doing this. Please see: > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html > > -Justin > > amit >> >> >> On Fri, Oct 9, 2009 at 5:39 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Amit Choubey wrote: >> >> Dear Gromacs Users, >> >> I have been trying to generate a larger lipid system but am >> running into troubles due to improper initial co-ordinates set >> up. Following are the steps i am trying to follow. >> >> 1. I start with a 128 dppc membrane and use genconf to create a >> larger system. I got the dppc128.pdb from Dr. Peter Tieleman's >> website. >> >> >> Did you correct for periodicity before you extended the system? The >> files distributed by Tieleman are compact representations. >> >> >> 2. I changed my topology file accordingly (change the number of >> DPPC and Water molecules) >> >> 3. I move on to energy minimization. During the mdrun i see the >> following message :- >> >> Warning: 1-4 interaction between 1854 and 1857 at distance 6.249 >> which is larger than the 1-4 table size 2.800 nm >> These are ignored for the rest of the simulation >> This usually means your system is exploding, >> if not, you should increase table-extension in your mdp file >> or with user tables increase the table size >> >> >> Looks to me like two bonded atoms are across the box from each >> other, which seems to answer my question above :) >> >> >> I also notice that the max force does not converge to less than >> 2000 rather its of the order of 2e+06 . >> >> 4. I tried to do energy minimization again on the above system >> but the steepest descent could not change the potential energy >> substantially and terminated after less that 20 steps. I again >> noticed the following warning >> Warning: 1-4 interaction between 1854 and 1857 at distance 5.269 >> which is larger than the 1-4 table size 2.800 nm >> These are ignored for the rest of the simulation >> This usually means your system is exploding, >> if not, you should increase table-extension in your mdp file >> or with user tables increase the table size >> >> 5. Now i changed my mdp files to do periodic_molecules = yes . >> Note pbc = xyz has been used as default. >> >> >> Bad idea. This option is for "infinite" molecules, like nanotubes >> or graphene sheets that are supposed to extend across the simulation >> box. >> >> >> Same warnings were printed out during energy minimization. >> >> 6. I also tried to use the table-extension option and increased >> its value to 10 nm but later the LINCS printed out too many >> warnings and MD could not be done. I know that its not at all a >> good idea to increase the 1-4 cut off. >> >> >> The standard advice is to fix the problem with the system, not >> change the table-extension. >> >> >> By the way to be specific the system size was 12 x 12 x 6 in >> nm3. I had 256 lipids and about 7300 water molecules. >> I believe that this might not be the best way to create a >> larger >> bilayer system. Could somebody suggest me other ways of doing this? >> >> >> Fix periodicity, then use genconf. >> >> -Justin >> >> Any help will be appreciated thank you >> >> Amit >> >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 <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 >
_______________________________________________ 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