When I find overlapping atom, what should I have to do? How is it possible to get solved?
Would you please help me? Sincerely, Shima ________________________________ From: Justin Lemkul <[email protected]> To: Shima Arasteh <[email protected]>; Discussion list for GROMACS users <[email protected]> Sent: Saturday, September 29, 2012 3:01 PM Subject: Re: [gmx-users] Energy minimization On 9/29/12 3:19 AM, Shima Arasteh wrote: > > Dear all, > > My system contains lipids, protein and water. > I want to energy minimize it, so ran grompp: > > > # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr > > and then: > # mdrun -v -deffnm em > > > The output is: > Steepest Descents: > Tolerance (Fmax) = 1.00000e+03 > Number of steps = 50000 > Step= 14, Dmax= 1.2e-06 nm, Epot= 2.30004e+17 Fmax= inf, atom= 518 > Stepsize too small, or no change in energy. > Converged to machine precision, > but not to the requested precision Fmax < 1000 > > Double precision normally gives you higher accuracy. > You might need to increase your constraint accuracy, or turn > off constraints alltogether (set constraints = none in mdp file) > > writing lowest energy coordinates. > > Back Off! I just backed up em.gro to ./#em.gro.3# > > Steepest Descents converged to machine precision in 15 steps, > but did not reach the requested Fmax < 1000. > Potential Energy = 2.3000388e+17 > Maximum force = inf on atom 518 > Norm of force = inf > > It seems that atome 518 has an infinite energy. So I tried to apply the > suggestion of turning off the constraints in em.mdp. To do so, I added > "constraints=none" to mdp file, But it doesn't make different. > > Any suggestion please? I don't know how to solve this problem. Please help me. > Atom 518 is overlapping with something nearby. You will have to visualize the system to identify the source of the problem. -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 list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
