[gmx-users] 1-4 interaction not within cut-off
Justin A. Lemkul
jalemkul at vt.edu
Fri Jun 4 21:51:40 CEST 2010
Rabab Toubar wrote:
> Hi Justin
>
> Thanks a lot for your prompt reply.
> The end of the em log file says:
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 10
>
> Double precision normally gives you higher accuracy.
>
> Steepest Descents converged to machine precision in 206 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy = -1.8784400e+05
> Maximum force = 7.9173694e+02 on atom 159
> Norm of force = 6.5868745e+03
>
OK, that all looks normal.
> And after em, I ran pr for 2ns and it went all good and you're correct
> it was for all bonds.
> After I read the manual and a couple of tutorial I understood that the
> PME is better for electrostatics but I am reproducing a reported work
> that used twin range cutoff of 1 for both vdw and electrostatics using
> 2fs time step and I want to see if I will get similar results. The
> authors stated that the simulations went well till the end of the 25 ns
> run! But seems that mine is crashing. Any suggestions?
>
If you have all the short-range cutoffs set to an equal value, that is decidedly
not a twin-range cutoff. Even the use of a proper twin-range setup does not
preclude the use of a long-range electrostatics method like PME. I would
suggest you look a bit more closely at the methods you're trying to reproduce.
I also suspect that you'll need constraints in order to use a 2-fs timestep.
-Justin
> Thanks
>
> Rabab Toubar
>
>
> --- On *Fri, 6/4/10, 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: "Gromacs Users' List" <gmx-users at gromacs.org>
> Date: Friday, June 4, 2010, 3:25 PM
>
>
>
> 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
> </mc/compose?to=jalemkul at vt.edu>>/* wrote:
> >
> >
> > From: Justin A. Lemkul <jalemkul at vt.edu
> </mc/compose?to=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 </mc/compose?to=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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>
--
========================================
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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