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 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 -- 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
