Please tell me where I am wrong. I downloaded pdb of chaps and used prodrg server to get .itp and .gro file. Then I checked .itp for any missing charge and I found it correct. Then I created 6.0x6.0x6.0 box with genbox inserting 7 molecules of chaps.gro. Then again using genbox and -maxsol I put 510 spc.itp in the box to get a density approaching 1. Then I did steepest descent energy minimization with constraints = none, for emtotal=2000 and emstep=3000. Up to this the gromacs runs fine. when I start simulated annealing for cooling at high pressure with constraint = all_bonds the programme gives fatal error linc warning and stops. If I do energy minimization with constraint =all_bonds then also with some error of linc wrning the minimization is completed. When I do minimization without adding water then there is no linc warning and minimization is completed but with final positive potential energy. Then as suggested by Justin I used smaller box and there also in simulated annealing stage the system gives linc warning and the programme stops with fatal error. Please tell me where I am wrong. shahid nayeem
On Fri, Jan 28, 2011 at 10:59 AM, Mark Abraham <[email protected]> wrote: > On 28/01/2011 3:51 PM, shahid nayeem wrote: >> >> 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. > > You've set up a system that isn't stable, but we don't have enough > information to have any idea why. "I tried with new box size" doesn't go > close to describing your method in enough detail for anyone to know where > you went wrong. > > See http://www.gromacs.org/Documentation/Terminology/Blowing_Up for generic > tips > > Mark > >> Please help. >> shahid Nayeem >> >> On Thu, Jan 27, 2011 at 7:06 PM, Justin A. Lemkul<[email protected]> 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 [email protected] >>> 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 [email protected]. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
