Dear Justin, Thank you for your kind reply! Hereby I attach a link to a screenshot of my RMSD.xvg file (In Step 9) Is it acceptable? The command line that I run is as follow:
1. pdb2gmx -ignh -ff gromos43a1 -f M1.pdb -o fws.pdb -p fws.top -water spce 2. editconf -bt cubic -f fws.pdb -o fws.pdb -d 1.0 3. genbox -cp fws.pdb -cs spc216.gro -o fws_b4ion.pdb -p fws.top 4. grompp -f em.mdp -c fws_b4ion.pdb -p fws.top -o ion.tpr -maxwarn 5 5. genion -s ion.tpr -o fws_b4em.gro -neutral -p fws.top -g ion.log -nname CL -nn 12 -pname NA+ 6. grompp -f em.mdp -c fws_b4em.gro -p fws.top -o em.tpr -maxwarn 5 7. mdrun -ntomp 8 -ntpi 1 -v -s em.tpr -deffnm em //Stepsize too small, or no change in energy. //Converged to machine precision, //but not to the requested precision Fmax < 100 //Steepest Descents converged to machine precision in 7559 steps, //but did not reach the requested Fmax < 100 //Potential Energy = -2.2999515e-08 //Maximum Force = 5.4296509e+02 on atom 2876 //Norm of Force = 4.8155560e+00 8. g_rms -s em.tpr -f em.trr -o rmsd_steep.xvg //select backbone for both - Option 4 9. xmgrace rmsd_steep.xvg & http://postimage.org/image/paojhlrtt/ Thanking you in advance! ________________________________ From: Justin Lemkul <[email protected]> To: Discussion list for GROMACS users <[email protected]> Sent: Monday, January 28, 2013 6:26 AM Subject: Re: [gmx-users] Steepest Descents converged to machine precision in 7559 steps, but did not reach the requested Fmax < 100. On 1/27/13 11:53 PM, Ewaru wrote: > Dear Gromacs experts, > > I am running gromacs for the first time, and this is my em.mdp file. > > define = -DFLEXIBLE > constraints = none > integrator = steep > dt = 0.01 ; ps ! > nstlist = 10 > ns_type = grid > rlist = 1.0 > coulombtype = PME > rcoulomb = 1.0 > vdwtype = cut-off > rvdw = 1.4 > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft = yes > DispCorr = EnerPres > nsteps = 10000 > nstenergy = 1000 > nstxtcout = 1000 > ; > ; Energy minimizing stuff > ; > emtol = 100.0 > emstep = 0.01 > > > Unfortunately, when running mdrun, I obtained this "Steepest Descents > converged to machine precision in 7559 steps, but did not reach the > requested Fmax < 100." > > Please, can somebody tell me what do I need to change in order for it to run > until the requested steps? Also, the RMSD graph obtained does not begins > from zero (how can I make it to?) and it does not converge. > http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision Regarding the RMSD, it probably won't converge during EM since the structure changes at every step. Without seeing your actual command and the snippet of the .xvg file showing the starting value, it's impossible to say why it doesn't start at zero. If it is a very small value (i.e. 1e-4 or less) and not exactly zero, you can consider that to be effectively zero. Just one of the quirks of floating-point math. -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 -- 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
