Dear Justin, I have run into another problem.
I created the system by including DHB in vwdradii.dat as follows: ; Very approximate VanderWaals radii ; only used for drawing atoms as balls or for calculating atomic overlap. ; longest matches are used ; '???' or '*' matches any residue name ; 'AAA' matches any protein residue name ??? C 0.15 ??? F 0.12 ??? H 0.04 ??? N 0.110 ??? O 0.105 ??? S 0.16 *DHB C 0.5 DHB H 0.5 DHB O 0.5* ; Water charge sites SOL MW 0 SOL LP 0 ; Masses for vsite construction GLY MN1 0 GLY MN2 0 ALA MCB1 0 ALA MCB2 0 VAL MCG1 0 VAL MCG2 0 ILE MCG1 0 ILE MCG2 0 ILE MCD1 0 ILE MCD2 0 LEU MCD1 0 LEU MCD2 0 MET MCE1 0 MET MCE2 0 TRP MTRP1 0 TRP MTRP2 0 THR MCG1 0 THR MCG2 0 LYSH MNZ1 0 LYSH MNZ2 0 After making this change, DHB molecules were not over lapping with each other. I tried to energy minimized the system. minim.mdp ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) ;emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; Short-range electrostatic cut-off rvdw = 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) constraints = none After about 6000 steps the run stops with the message: 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. Steepest Descents converged to machine precision in 6012 steps, but did not reach the requested Fmax < 10. Potential Energy = 1.0655116e+05 Maximum force = 1.6512177e+02 on atom 2076 Norm of force = 6.5337501e+00 The potential energy is high, but I still continued to equilibration. After NVT equilibration, NVT equilbration runs into the following error as soon it starts: Warning: 1-4 interaction between 4512 and 4516 at distance 6.148 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size /var/spool/pbs/mom_priv/jobs/1869547.lionxj.rcc.psu.edu.SC: line 14: 2359 Segmentation fault mdrun -deffnm npt So, I have three questions: 1. Is the starting structure bad? 2. Did I change the vdwd radii by a lot (0.105 to 0.5) 3. What value of table extension should be used for 1-4 interaction ( default value is?) if thats the problem to be fixed. Please guide. Thanks, SN On Tue, Jun 14, 2011 at 11:29 AM, shivangi nangia <shivangi.nan...@gmail.com > wrote: > 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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