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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