Re: [gmx-users] EM error
Everytime I remove the atom that is causing the INF force, it gives me new atom that causes INF force. (The ones that come up are all water beads that are causing the infinite force), does that mean when i did genbox it inserted water incorrectly? (Because I viewed it in VMD it's certainly not overlapping with my solute. ) Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 8:12 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: Dear users, Now I fixed the initial structure error, and I solvated it in water (martini bead model), and i run typical EM, I get the following error: Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=5 Step= 14, Dmax= 1.2e-06 nm, Epot= 4.48322e+19 Fmax= inf, atom= 14524 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. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = 4.4832208e+19 Maximum force =inf on atom 14524 Norm of force =inf gcq#182: That Was Cool (Beavis and Butthead) -My EM.mdp file contains the following: integrator = steep dt = 0.020 nsteps = 5 ;Note: 100 steps is to much for a vacuum run (nsteps=10) nstlog = 1000 nstenergy= 500 nstxtcout= 500 nstlist = 10 ns_type = grid pbc = xyz periodic_molecules = no rlist= 1.4 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r= 15 epsilon_rf = 1 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 My system size 73191 W, and 1 star (consisted of 101 atoms) I read somewhere that it's that atom 14524 is overlapping… I can't visually see anything complicated in my VMD since the system is pretty big Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- gmx-users mailing listgmx-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 listgmx-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
Re: [gmx-users] EM error
On 1/9/13 8:42 PM, Xu Dong Huang wrote: Everytime I remove the atom that is causing the INF force, it gives me new atom that causes INF force. (The ones that come up are all water beads that are causing the infinite force), does that mean when i did genbox it inserted water incorrectly? (Because I viewed it in VMD it's certainly not overlapping with my solute. ) It seems like all the waters are being placed too close to the polymer beads, so you should probably increase the value of -vdwd when running genbox. You can make your life easier in visualization by selecting only certain atoms to display, i.e. by using the Tk console: set myatoms [atomselect 0 (within 5 of index 14523)] animate write pdb myfile.pdb sel $myatoms That saves the coordinates of any atom within 5 Angstrom of the problematic atom below (14524, or index 14523). Displaying these atoms only can be much more useful than trying to sift through 7+ atoms. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 listgmx-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
Re: [gmx-users] EM error
@ Justin, Thank you, that worked like a charm! (Using increased vanderwal distance) Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 8:42 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: Everytime I remove the atom that is causing the INF force, it gives me new atom that causes INF force. (The ones that come up are all water beads that are causing the infinite force), does that mean when i did genbox it inserted water incorrectly? (Because I viewed it in VMD it's certainly not overlapping with my solute. ) Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 8:12 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: Dear users, Now I fixed the initial structure error, and I solvated it in water (martini bead model), and i run typical EM, I get the following error: Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=5 Step= 14, Dmax= 1.2e-06 nm, Epot= 4.48322e+19 Fmax= inf, atom= 14524 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. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = 4.4832208e+19 Maximum force =inf on atom 14524 Norm of force =inf gcq#182: That Was Cool (Beavis and Butthead) -My EM.mdp file contains the following: integrator = steep dt = 0.020 nsteps = 5 ;Note: 100 steps is to much for a vacuum run (nsteps=10) nstlog = 1000 nstenergy= 500 nstxtcout= 500 nstlist = 10 ns_type = grid pbc = xyz periodic_molecules = no rlist= 1.4 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r= 15 epsilon_rf = 1 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 My system size 73191 W, and 1 star (consisted of 101 atoms) I read somewhere that it's that atom 14524 is overlapping… I can't visually see anything complicated in my VMD since the system is pretty big Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- gmx-users mailing listgmx-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 listgmx-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 listgmx-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
