[gmx-users] 1-4 interaction not within cut-off
Justin A. Lemkul
jalemkul at vt.edu
Sat Jun 5 02:25:04 CEST 2010
Rabab Toubar wrote:
> they are stating explicitly that it is a twin range cutoff
> the manual states that
> "vdwtype:
> Cut-off
> Twin range cut-off’s with neighbor list cut-off rlist and VdW
> cut-off rvdw, where
> rvdw ≥ rlist."
> "coulombtype:
> Cut-off
> Twin range cut-off’s with neighborlist cut-off rlist and
> Coulomb cut-off rcoulomb, where rcoulomb ≥ rlist."
>
> because rlist is not stated so I left it as default value 1nm according
> to the manual because rcoulomb and rvdw can both be ≥ rlist.
These are generalizations. Since a plain cutoff is essentially a special case
of a twin-range cutoff, then it can be stated that cutoffs are "twin range."
If rlist=rcoulomb=rvdw you most certainly do not have a twin-range nonbonded
setup. It is a plain truncation. Please consult some basic textbook material
for the theory and proper implementation of a twin-range cutoff scheme.
>
> the authors didn't set any constraints, and I didn't use any. For the
> restraints I used pr.mdp and this step went well.
>
They most certainly did set constraints! From the text you quoted:
"...time step for all simulations is 2fs and LINCS method was used to constrain
bonds lengths."
> Is there any changes I can do for the md.mdp while sticking to the
> paper's methods, like may be increasing the table-extension as it was
> suggested in the error message?
Never adjust the table-extension parameter. The simple fact is that your system
is blowing up, and no amount of coaxing this parameter into cooperation will fix
broken model physics. I see two possibilities for fixing the instability:
1. Use constraints with a 2-fs timestep
2. Do not use a plain Coulombic cutoff. Use PME. I understand you're trying to
follow a previously-described methodology, but the text you quoted simply
neglects long-range interactions, both LJ and Coulombic. Twin-range cutoffs
apply to short-range interactions, and do not preclude the use of a stable
long-range method like PME.
>
> And if I want to define the electrostatics properly, is there anything
> more than setting the coulombtype for electrostatics as PME? or this
> would be only for short range electrostatics and another term is used
> for long range elecrtrostatics?
>
PME is a long-range method, dealing with terms that fall beyond rcoulomb.
Anything within rcoulomb is short-range.
> I know I won't learn GMX in a few days, but I am trying to get all the
> help that I could get
>
If you're just starting out, then textbook reading and tutorials are absolutely
requisite. I would also recommend trying to find a paper with more detailed
methodology. IMHO, the text you quote leaves out several important details,
making the results difficult to reproduce.
-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, 4:49 PM
>
>
>
> 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
> </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, 3:51 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>
> > </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: "Gromacs Users' List" <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: 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>>
> > > </mc/compose?to=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>>
> > > </mc/compose?to=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>>
> > </mc/compose?to=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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--
========================================
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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