Re: [gmx-users] why minimization stop so fast
On 4/16/13 1:05 PM, Albert wrote: Hello: I've built a system with CHARMM-GUI, and I am trying to mimize it with following em.mdp file title = steepest descent energy minimization define = -DPOSRES -DPOSRES_LIG cpp = /usr/bin/cpp include = integrator = steep nsteps = 5 emtol = 0.01 nstcgsteep = 1000;step for cg correction ,the larger the more accurate nstxout = nstvout = nstlog = 100 nstenergy = 10 nstxtcout = 100 nstlist = 10 ns_type = grid rcoulomb= 1.4 coulombtype = pme fourierspacing= 0.12 pme_order= 4 rvdw= 1.4 rlist = 1.4 DispCorr= enerpres constraints = none; none,hbonds,all-bonds,h-angles,all-angles cutoff-scheme =Verlet ; GPU running constraint_algorithm = Lincs but it stopped after 15 steps. Steepest Descents: Tolerance (Fmax) = 1.0e-02 Number of steps=5 Energy minimization has stopped, but the forces havenot converged to the requested precision Fmax 0.01 (whichmay not be possible for your system). It stoppedbecause the algorithm tried to make a new step whose sizewas too small, or there was no change in the energy sincelast step. Either way, we regard the minimization asconverged to within the available machine precision,given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, butthis is often not needed for preparing to run moleculardynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) 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 0.01. Potential Energy = 3.4943549e+18 Maximum force =inf on atom 23533 Norm of force =inf NOTE: 22 % of the run time was spent in domain decomposition, 6 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) gcq#154: Rub It Right Accross Your Eyes (F. Zappa) Your system has severe atomic overlap. You have infinite force on atom 23533. -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] why minimization stop so fast
Hi Justin: thanks for kind reply. Yes, there many atom clashes in CHARMM-GUI system, so I add very strong force on protein and ligands, and try to minimize the rest of the system do you have any idea how can I solve the issue and make it work? thanks a lot Albert On 04/16/2013 07:09 PM, Justin Lemkul wrote: Your system has severe atomic overlap. You have infinite force on atom 23533. -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] why minimization stop so fast
On 4/16/13 1:13 PM, Albert wrote: Hi Justin: thanks for kind reply. Yes, there many atom clashes in CHARMM-GUI system, so I add very strong force on protein and ligands, and try to minimize the rest of the system do you have any idea how can I solve the issue and make it work? Create a more physically reasonable starting structure. -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] why minimization stop so fast
On 04/16/2013 07:28 PM, Justin Lemkul wrote: Create a more physically reasonable starting structure. -Justin the protein and ligand are already minimized, but CHARMM-GUI create the mix lipids automatically which I cannot change them. ALBERT -- 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] why minimization stop so fast
On 4/16/13 1:31 PM, Albert wrote: On 04/16/2013 07:28 PM, Justin Lemkul wrote: Create a more physically reasonable starting structure. -Justin the protein and ligand are already minimized, but CHARMM-GUI create the mix lipids automatically which I cannot change them. Then you will have to find a better method for creating the membrane or otherwise determine how you might modify then one with which you've been provided. -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
