I forgot to mention that when I prepared urea_water box then also I got similar box of water in one region and urea in other region separated from it. But on minimization and following simulated annealing and equilibration I got a uniformly mixed urea water box. Shahid Nayeem
On Thu, Jan 27, 2011 at 12:30 PM, shahid nayeem <msnay...@gmail.com> wrote: > Hi Mark > Thanks. > I created a box of 6x6x6 inserting 7 molecule of chaps with genbox.Then I > solvated this box with genbox using -maxsol 500 and spc216.gro. On > visualization, at this stage itself uniform solvation did not occur and I > got water in one region and chaps molecule spread throughout box but not > inside water. I should have visualized it earlier before going for > minimization. Please help me. > shahid Nayeem > > On Thu, Jan 27, 2011 at 11:36 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > >> >> >> On 01/27/11, *shahid nayeem * <msnay...@gmail.com> wrote: >> >> Dear All >> I am trying to prepare a solvation box of chaps. After generating .itp and >> .gro at ProDrg and thorough check of charges, I started with a box size of >> 6x6x6. Energy minimization, simulated annealing (Cooling under high pressure >> and again heating at normal pressure) as well as final equilibration ran >> smoothly. But finally I get a box where all water molecules get accumulated >> in two three small region within the box and all chaps molecules gets >> accumulated in another small regions.I wanted near random uniform >> distribution of chaps in water. Any help from user, where I am wrong and >> what should I do. >> >> >> You haven't told us how you've solvated the system (e.g. with genbox), >> that it looked OK when you visualized it between each step, and that you're >> sure your observations cannot be rationalized as a periodicity artefact. >> >> Mark >> -- >> 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 >> > >
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