18 okt 2012 kl. 12.08 skrev Ali Alizadeh: > Dear All users > > 1- I have a symmetric simulation box but i can not produce a symmetric > number density result (number density vs. z direction(nm)) > > My simulation box is orthorhombic. My boundary condition is pbc but i > don't perform any commands before final run for > > Preparation of simulation box(related to pbc) and Just, in my input > file(.mdp file) select pbc xyz-option. > > 1- construction of simulation box with a software > 2- pdb2gmx for producing .gro and .top > 3- energy minimization > 4- nvt(it converged) > 5- npt(it converged) > 6- production of md(2 nano second) > > 2- I don't locate the centre of masses. How can i determine it?Is it > necessary? >
The center of mass is undefined for a periodic system. > -- > Sincerely > -- > 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 Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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
