Hi Justin, Thanks for the reply. When I tried to gmxcheck the minimization process I got an error:
Timesteps at t=810 don't match (2, 1) Timesteps at t=814 don't match (1, 2) Timesteps at t=816 don't match (2, 1) Timesteps at t=818 don't match (1, 2) till the end of the run, that is why I thought the system is not properly minimized. I will look into how to check the Potential Energy. the em.mdp file is as follows: cpp = /usr/bin/cpp ; the c preprocessor define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 ;ps ie 2 fs! nsteps = 1000 nstlist = 10 ns_type = grid rlist = 1.0 ;short range coulombtype = cut-off rcoulomb = 1.0 rvdw = 1.0 vdwtype = cut-off fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes emtol = 10 emstep = 0.01 the md.mdp file is: cpp = /usr/bin/cpp constraints = none ;* integrator = md dt = 0.002 ; ps ! nsteps = 12500000 ; total 25 ns;* nstcomm = 1 nstxout = 500 ; collect data every 1 ps nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = cut-off rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.0 ;* fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 ; ps compressibility = 4.5e-5 ; bar-1 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 621432 Any suggestions are appreciated Thanks Rabab Toubar --- On Thu, 6/3/10, Justin A. Lemkul <jalem...@vt.edu> wrote: From: Justin A. Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] 1-4 interaction not within cut-off To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Date: Thursday, June 3, 2010, 4:37 PM Rabab Toubar wrote: > Hi, > > I set my .mdp file to minimize the system for 1000 steps, but it stopped at > ~200 saying: "Stepsize too small, or no change in energy. > Converged to machine precision, but not to the requested precision Fmax < 10" > but the molecule is now outside the box > This is not really a problem, provided that both the potential energy and Fmax that resulted are reasonable.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 > I did position restraint for 2ns using LINCS, and things went well > > running md, it ran for only 0.3 ns out of 30, and I got an error message that > 1-4 interaction between 2 atoms are at a distance > table-size (1nm) with a > suggestion to increase the table-extension in mdp file. > I checked > http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off > suggesting reminimizing. > The other possibility is that your .mdp settings are inappropriate, but you haven't provided that information. > My question is: is it OK that the system doesn't minimize till the end of the > specified number of steps? is it OK to be outside the box as long as you > assign boundary conditions as in case of NAMD? and what is the best option - > you think - I have to solve the md problem > Whether or not you need to revisit the EM procedure depends on how well it actually did (see comment above). The periodicity effect is a non-issue, since there is no "outside" of a periodic box. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin > Any suggestions are highly apprecitaed > Rabab > > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php
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