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 /<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, 3:51 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 /<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: "Gromacs Users' List" <gmx-users@gromacs.org
</mc/compose?to=gmx-us...@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>
> </mc/compose?to=jalem...@vt.edu
</mc/compose?to=jalem...@vt.edu>>>/* wrote:
> >
> >
> > From: Justin A. Lemkul <jalem...@vt.edu
</mc/compose?to=jalem...@vt.edu>
> </mc/compose?to=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>
</mc/compose?to=gmx-us...@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
> >
> > ========================================
> > -- gmx-users mailing list gmx-users@gromacs.org
</mc/compose?to=gmx-us...@gromacs.org>
> </mc/compose?to=gmx-us...@gromacs.org
</mc/compose?to=gmx-us...@gromacs.org>>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
http://www.gromacs.org/search before
> > posting!
> > Please don't post (un)subscribe requests to the list.
Use the www
> > interface or send it to gmx-users-requ...@gromacs.org
</mc/compose?to=gmx-users-requ...@gromacs.org>
> </mc/compose?to=gmx-users-requ...@gromacs.org
</mc/compose?to=gmx-users-requ...@gromacs.org>>.
> > Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
> >
> >
>
> -- ========================================
>
> 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@gromacs.org
</mc/compose?to=gmx-us...@gromacs.org>
> </mc/compose?to=gmx-us...@gromacs.org
</mc/compose?to=gmx-us...@gromacs.org>>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org
</mc/compose?to=gmx-users-requ...@gromacs.org>
> </mc/compose?to=gmx-users-requ...@gromacs.org
</mc/compose?to=gmx-users-requ...@gromacs.org>>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
-- ========================================
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@gromacs.org
</mc/compose?to=gmx-us...@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
</mc/compose?to=gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
