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.
amit On Fri, Oct 9, 2009 at 5:39 PM, Justin A. Lemkul <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 >> 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 >> > > -- > ======================================== > > 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
