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 /<jalem...@vt.edu>/* wrote:
From: Justin A. Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] 1-4 interaction not within cut-off
To: "Gromacs Users' List" <gmx-users@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 /<jalem...@vt.edu
</mc/compose?to=jalem...@vt.edu>>/* wrote:
>
>
> From: Justin A. Lemkul <jalem...@vt.edu
</mc/compose?to=jalem...@vt.edu>>
> Subject: Re: [gmx-users] 1-4 interaction not within cut-off
> To: "Discussion list for GROMACS users"
<gmx-users@gromacs.org </mc/compose?to=gmx-us...@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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