Hi Justin Thanks a lot. I tried doing energy minimization and th lowering emtotal to 200 and the system converged to Steepest Descents converged to Fmax < 200 in 1411 steps Potential Energy = -3.9063050e+05 Maximum force = 1.3442458e+02 on atom 927 Norm of force = 1.4758101e+01 For equilibration of solvation box I am following a biophys j paper in which protocol for urea box preparation is given. A simulated annealing under high pressure (ref_p=100) to cool system from 300 to 0K thereafter heating back to 300K at ref_p=1. Again 1ns MD at same condition. If this way is harsh treatment of system then suggest me the way out. My sa.mdp sa_hot.mdp and sa_equilibriation.mdp as well as chaps.itp are attached with this mail Shahid Nayeem On Mon, Jan 31, 2011 at 9:47 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > shahid nayeem wrote: >> >> 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 > > PRODRG doesn't have a problem of missing charges. It provides notoriously > incorrect charges. > >> 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 > > These settings make no sense. An emtol of 2000 is very high, and emstep of > 3000 is total nonsense. How well did you EM converge? What were the values > of the potential energy and maximum force? > >> 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. > > How about simplifying the problem. Does the system run under normal > conditions? In other words, can you run normal MD? You're treating the > system very harshly with the combination of high pressure and annealing. > Without seeing your .mdp file for this process, it's impossible to say how > reasonable your settings are. > > It is also possible that your parameters for CHAPS (if they are the default > ones from PRODRG) are incorrect. The charges and charge groups nearly > always are. Without seeing them, there's nothing better to offer. > > -Justin > >> shahid nayeem >> >> On Fri, Jan 28, 2011 at 10:59 AM, Mark Abraham <mark.abra...@anu.edu.au> >> 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<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 >>> > > -- > ======================================== > > 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 >
sa.mdp
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