[gmx-users] 1-4 interaction not within cut-off
Justin A. Lemkul
jalemkul at vt.edu
Fri Jun 4 22:49:21 CEST 2010
Rabab Toubar wrote:
> 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."
This is not fully explained. The value of rlist is not given, but based on this
information, I would not conclude that this is a twin-range cutoff - the values
are the same, so there are not two interaction ranges!
> "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
I would not recommend following this part of the protocol. Coupling ions
separately from the solvent often leads to instability:
http://www.gromacs.org/Documentation/Terminology/Thermostats
> 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. "
Make sure that you understand that constraints and restraints are different things:
http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints
By removing the restraints, it should not be inferred that the constraints were
removed as well.
The absence of any information about long-range electrostatics is also somewhat
troubling. A plain cutoff is not generally recommended.
-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, 3:51 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
> </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: "Gromacs Users' List" <gmx-users at gromacs.org
> </mc/compose?to=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>
> > </mc/compose?to=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>
> > </mc/compose?to=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>
> </mc/compose?to=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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--
========================================
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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