Dears, I changed the coordinates of overlapping atoms and got a normal potential energy. Then when I go to the next step ( NVT equilibrium ), it doesn't run and I just get some pdb files. How is it possible to find the problem?
It might be clashes in the system but How can I find the overlapping atoms and the reason of clashe among a vast number of atoms? Sincerely, Shima ----- Original Message ----- From: Peter C. Lai <p...@uab.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com> Cc: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Sunday, December 16, 2012 11:18 AM Subject: Re: [gmx-users] Energy minimization Probably remove the overlapping lipid then. Once you run MD it will repack. On 2012-12-15 09:19:49PM -0800, Shima Arasteh wrote: > Thanks for your kind reply. > My system is composed of protein packed by lipids. The atoms overlapping, are > protein ( atom 288) and lipid chain. I think if I move them, I may get some > other clashes, may I not? > Any other suggestion? > > Thanks. > > > > Sincerely, > Shima > > > ----- Original Message ----- > From: Peter C. Lai <p...@uab.edu> > To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS > users <gmx-users@gromacs.org> > Cc: > Sent: Sunday, December 16, 2012 8:44 AM > Subject: Re: [gmx-users] Energy minimization > > It depends on what the atom is overlapping with and some conjecture as to > what might be causing the overlap: > > You can always manually move it, either by editing the .gro file directly > or using a tool like VMD to move it or the molecule/fragment it's attached to > with the mouse and then display the new coordinates and the update the .gro > file. > If it's something like a solvent molecule (water/lipid) and there is nowhere > to move the molecule, you can try deleting it too (just remmeber to update > .top file). > > On 2012-12-15 08:58:59PM -0800, Shima Arasteh wrote: > > 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 <jalem...@vt.edu> > > To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for > > GROMACS users <gmx-users@gromacs.org> > > 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 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 > > -- -- -- 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
