[gmx-users] 1-4 interaction not within cut-off
Rabab Toubar
rtoubar at yahoo.com
Fri Jun 4 22:41:23 CEST 2010
Well all the relevant info from m&m is attached below. I tried to contact the author with no reply!. Ref: Journal of Biomolecular Structure & Dynamics, ISSN 0739-1102
Volume 27, Issue Number 4, (2010)
"The GROMACS 3.3.3 simulation package (www.gromacs.org) was used for all the simulations with ffG45a3 force field. The SPC water model was used in the simulations. Periodic boundary conditions were applied to the system. A twin range cut-off of 1.0 nm for van der Waals and Coulomb interactions were used."
"All simulations were performed at a constant temperature of 300 K using Berendson barostat with isotropic coupling constant of τp 5 0.5 ps, compressibility equal to 4.5 3 10-5 bar-1 and time constants equal to 0.1 ps for the three groups i.e., protein, solvent and Cl-. Integration time step for all simulations is 2fs and LINCS method was used to constrain bonds lengths. The structures were energy minimized for 1000 steps using steepest descent prior to the MDS setup. Positional restraints were applied to the protein (all-bonds) with a force constant of 1000 kJ mol-1 for 2 ns to enable the relaxation of water molecules around the protein. All restraints were then removed, and the simulations were carried out. "
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, 3:51 PM
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
>
> ========================================
> -- gmx-users mailing list gmx-users at gromacs.org
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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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