Thanks Justin I tried with new box size of 2.8x2.8x2.8 . During energy minimization with steepest descent to force of 2000 and constraint=none, the system converged in 754 steps with positive potential energy. In subsequent simulated annealing with constraint all bonds it starts giving link warning in 0 step with rms 7407.805164, max 66989.116545 (between atom 94 and 117) and a list of bond thar rotated more than 30 degree almost atom number belonging to chaps molecule. Please help. shahid Nayeem
On Thu, Jan 27, 2011 at 7:06 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > shahid nayeem wrote: >> >> Dear All >> >> I am sending this mail again on user list because my reply to Mark’s >> query was not uploaded on the list. >> >> Original messge: >> >> 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. >> >> Reply to query. >> >> I created a box of 6x6x6 inserting 7 molecule of chaps with (genbox >> –ci 7 chaps.gro).Then I solvated the output box with genbox using >> -maxsol 500 and spc216.gro. On visualization, at this stage itself >> uniform solvation did not occur (I got water in one region and chaps >> molecule in other region) but I observed a similar situation while > > If your box was not completely solvated, then don't use -maxsol. A box of > 6x6x6 nm should require more than 500 molecules of water to fill. If you're > trying to achieve some specific mole fraction or concentration, then > re-figure your box size. > > -Justin > >> preparing 10M urea salvation box. This was followed by 1ns simulated >> annealing from temp 300K to 0K and pressure 100 bar, then 1ns >> simulated annealing from temp. 0k to 300k and then ins equilibriation >> at this temperature. In case of urea finally I got uniformly solvated >> urea_water_box but in chaps I couldn’t get it. >> >> Shahid Nayeem > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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
