I run the same mdp files for glucose in vaccum. I ma geting the proper results, I can visualize the strucutre properly in VMD.
If I use same for water why I am not geting proper structure ? Nilesh On Fri, May 20, 2011 9:48 am, Erik Marklund wrote: > Exactly. So now is the time for skillful scripting. > > > Erik > > > Nilesh Dhumal skrev 2011-05-20 15.31: > >> I used the same topology file to run 256 water molecules simulation and >> I >> got the proper result (compared with reported one). >> >> The problem is to visualize the trajectory in VMD since gromacs fails >> to write valid pdb files when the coordinates are too large. >> >> Nilesh >> >> >> >> On Fri, May 20, 2011 5:22 am, Erik Marklund wrote: >> >>> Justin A. Lemkul skrev 2011-05-19 22.42: >>> >>> >>>> >>>> Vitaly Chaban wrote: >>>> >>>> >>>>>> For vacuum systems, "pbc = no" in conjunction with zero cutoffs >>>>>> is correct to obtain a gas-phase system. >>>>> >>>>> For reasonably large box, this is the same heck. >>>>> >>>>> >>>>> >>>> Setting a box size and using "pbc = xyz" precludes the use of >>>> infinite cutoffs, which should be the most rigorously correct way to >>>> treat this type of system. With PBC, there are long-range effects >>>> that should be avoided. >>>> >>>>> Nilesh: visualize your system, using VMD or ngmx. The behavior of >>>>> your molecular cluster during the first ps will provide an >>>>> answer. Are you sure that your topology is healthy? >>>>> >>>> I agree with this. The system should be going absolutely haywire >>>> :) >>>> >>>> >>>> >>>> -Justin >>>> >>>> >>>> >>> Yes, this is a good test, and the topology should be inspected. >>> However, >>> the observed result is expected for this system. A water dimer coupled >>> to a thermostat will dissociate eventually (pretty rapidly) at 300 K. >>> The water >>> molecules themselves seem intact. The problem with visualization comes >>> from the fact that gromacs fails to write valid pdb files when the >>> coordinates are too large. I called this a bug on the developer list >>> one or two years ago since this generates pdb files that gromacs >>> itself can't read, but the other developers didn't catch on. You can >>> postprocess the pdb and cap the coordinates so that they're confined >>> to the range that the pdb format allows, but note that this will mess >>> up the water moleucles as they get very far apart. >>> >>> Erik >>> >>> >>> >>> -- >>> ----------------------------------------------- >>> Erik Marklund, PhD student >>> Dept. of Cell and Molecular Biology, Uppsala University. >>> Husargatan 3, Box 596, 75124 Uppsala, Sweden >>> phone: +46 18 471 4537 fax: +46 18 511 755 >>> er...@xray.bmc.uu.se http://folding.bmc.uu.se/ >>> >>> -- >>> 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/Support/Mailing_Lists/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/Support/Mailing_Lists >>> >>> >>> >>> >> > > > -- > ----------------------------------------------- > Erik Marklund, PhD student > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 4537 fax: +46 18 511 755 > er...@xray.bmc.uu.se http://folding.bmc.uu.se/ > > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists