Thanks. So in this case no matter what density I will start with e.g. 480 kg/m3 presuming the force filed is correct I should get at given conditions the density of interest?
Steven On Mon, Mar 18, 2013 at 10:34 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/18/13 6:14 PM, Steven Neumann wrote: >> >> On Mon, Mar 18, 2013 at 8:40 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>> >>> On 3/18/13 2:56 PM, Steven Neumann wrote: >>>> >>>> >>>> Dear Gmx Users, >>>> >>>> I am trying to obtain given density for my system for a given molecule >>>> - its a cubic box of 5 nm in dimension. >>>> >>>> I calculated that I need 850 molecules to get the density of 500 g/mol >>>> In my box there is already 1 molecule so I try: >>>> >>>> genbox -cp Box.pdb -ci molecule.pdb -nmol 849 -o BoxMol.pdb >>>> >>>> >>>> >>>> Added 819 molecules (out of 849 requested) >>>> Output configuration contains 9020 atoms in 820 residues >>>> Volume : 125 (nm^3) >>>> Density : 480.336 (g/l) >>>> Number of SOL molecules: 0 >>>> >>>> How can I add 30 more molecules using gromacs? I want to avoid adding >>>> it manually. >>>> >>> >>> Use a larger box and equilibrate. >> >> >> Thanks. >> Larger box will need more molecules which is quite obvious so the same >> problem occurs. I need a cubic box first with given fixed density and >> then equilibrate it. Further step is to extend the box in one >> dimension to get properties I want. >> Shall manually add them then? >> > > I think you missed the point of what I was saying. You can use a larger > box, with 850 molecules inserted, and equilbrate under NPT (using isotropic > pressure coupling to guarantee the box stays cubic). Provided the force > field model produces the density you want, that's all you need to do. > > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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/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
