Thanks Justin, vdwradii.dat suggestion worked :)
On Mon, Jun 13, 2011 at 11:05 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > shivangi nangia wrote: > >> Hello dear gmx-users, >> >> I am trying to create a system which has 2,5-dihydobenzoic acid (DHB) as >> the solvent ( with a positively charged protein and few DHB anions) in a >> box. >> >> I have created the .itp and .gro file of DHB using PRODRG. >> >> > Unrelated advice - the topology is probably useless unless you've corrected > the charges. See the paper linked from: > > http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips > > > I am able to create the system, but when I try to energy minimize the >> system I get the message: >> >> Steepest Descents: >> Tolerance (Fmax) = 1.00000e+01 >> Number of steps = 50000 >> Step= 14, Dmax= 1.2e-06 nm, Epot= 9.04353e+19 Fmax= inf, atom= >> 2781 >> Stepsize too small, or no change in energy. >> Converged to machine precision, >> but not to the requested precision Fmax < 10 >> >> Double precision normally gives you higher accuracy. >> >> writing lowest energy coordinates. >> >> Back Off! I just backed up em.gro to ./#em.gro.1# >> >> Steepest Descents converged to machine precision in 15 steps, >> but did not reach the requested Fmax < 10. >> Potential Energy = 9.0435262e+19 >> Maximum force = inf on atom 2781 >> Norm of force = inf >> >> >> The reason behind this was that DHB molecules were on top of each other, >> highly dense system ( viewed in VMD) >> So, to reduce the density of DHB molecules, I tried using-vdwd option of >> genbox (changed from default value of 0.105 to 0.5) >> But, I got almost same number of DHB molecules using genbox. >> >> > The -vdwd option has no effect unless you're using atom names that are not > found in vdwradii.dat (see the genbox help description). Your DHB molecule > should be unaffected by the use of -vdwd. > > > >> What is the best solution to this problem as I understand, reducing the >> density of DHB molecules around the protein as a solvent or there is some >> other problem? >> >> > You need to generate a configuration in which molecules aren't overlapping. > There are several ways to accomplish this. You can manually place molecules > within a box at a desired location with editconf -center, otherwise genbox > -ci -nmol. If the locations of the molecules are not what you desire with > genbox, change the value of -seed and try again. > > -Justin > > -- > ======================================== > > 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 >
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