[gmx-users] 1-4 interaction not within cut-off
Justin A. Lemkul
jalemkul at vt.edu
Fri Jun 4 21:25:35 CEST 2010
Rabab Toubar wrote:
> 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.
>
When running EM, mdrun prints the important information out at the very end,
both to the screen and to the end of the .log file.
> 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 !
Using a 2-fs timestep without constraints may not be stable. Your original
message said you ran 2 ns of position restrained MD with LINCS, which I assumed
meant that you were constraining the bond lengths. If you actually did this,
what reason do you have for turning off the restraints after equilibrating?
> 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
Using a plain cutoff for electrostatics can lead to a number of artefacts. I
see no reason to use this method in favor of other, more advanced and accurate
methods.
-Justin
> 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 /<jalemkul at vt.edu>/* wrote:
>
>
> From: Justin A. Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] 1-4 interaction not within cut-off
> To: "Discussion list for GROMACS users" <gmx-users at 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
>
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--
========================================
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
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