[gmx-users] RE: System instability with switched cut-off
Matteus Lindgren
matteus.lindgren at chem.umu.se
Fri Aug 7 15:51:47 CEST 2009
Thanks for the answer. PME can't be used since the interaction coulomb LR
value between two groups can't be extracted for PME. I know switched cutoffs
produce artefacts around the cutoff value but in this case I am more
interested in the correct interaction energies than the correct forces which
is why a shifted function can't be used. My plan was that with the rather
large rcoulomb and rlist values I chose, a switched function would be ok.
Would the reaction field method suit my purposes? How do I choose
epsilon_rf? I have pure water and 10M urea as solvents. Still I would like
to figure out why switch creates these enormous fluctuations in my system.
Can you see any errors in the parameters I've listed?
Matteus
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Today's Topics:
1. RE: System instability with switched cut-off (Berk Hess)
2. Re: Energy Minimisation and Equilibration Problems (Bruce D. Ray)
3. Re: question about mdrun -append (Baofu Qiao)
----------------------------------------------------------------------
Message: 1
Date: Fri, 7 Aug 2009 13:46:31 +0200
From: Berk Hess <gmx3 at hotmail.com>
Subject: RE: [gmx-users] System instability with switched cut-off
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <COL113-W42EEC13FE2DE71D0118E668E0B0 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
Never ever use switched cut-off's!
Switched cut-off's can give extremely strong artifacts.
In 4.1 grompp will warn you about this.
Switch gives you correct energies at short range, but incorrect forces
in the switching region.
What you want is correct forces up to (nearly) the cut-off.
Shift does this.
But reaction-field does this smoother and it even has a physical
interpretation.
So use RF if you can not use PME.
But why can't you use PME, you have pbc, right?
Berk
From: matteus.lindgren at chem.umu.se
To: gmx-users at gromacs.org
Date: Fri, 7 Aug 2009 13:13:24 +0200
Subject: [gmx-users] System instability with switched cut-off
Dear all
Im trying to extract the interaction
energies between protein and solvent. Since PME cant be used for this, plain
cutoffs causes problems and shifted cut-offs gives incorrect energies I want
to
use switched cutoff but with rather long cutoffs to get the correct energy.
Unfortunately my system is unstable and
within a few ps the total energy and kinetic energy fluctuates several
hundred
per cent. I4ve tried different options but can4t get it to stabilize except
if
I4m using any other coulomb type. Any ideas?
title =
Dyna
cpp =
/usr/bin/cpp
constraints =
hbonds
integrator =
md
dt =
0.002
nsteps =
20000000
nstxout =
20000000
nstvout =
20000000
nstfout =
5000
nstlog =
250
nstenergy =
500
nstxtcout =
500
xtc_grps =
energygrps =
polar hydrophobic peptide SOL
nstlist = 1
ns_type =
grid
coulombtype =
switch
rcoulomb_switch =
1.4
rcoulomb =
1.7
rlist =
2.0
vdwtype =
switch
rvdw_switch =
1.4
rvdw =
1.7
tcoupl =
nose-hoover
tc-grps = Protein
Non-Protein
tau_t =
0.5 0.5
ref_t =
298 298
Pcoupl =
parrinello-rahman
tau_p =
1.0
compressibility =
4.5e-5
ref_p =
1.0
;disre_fc =
30
gen_vel = yes
gen_temp = 298
gen_seed = 173529
unconstrained_start
= no
Thanks
Matteus
---------------------------------------------------------
Matteus
Lindgren, graduate student
Department of Chemistry, Umee University
SE-901 87 Umee, Sweden
Phone: +46 (0)90-7865368
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Message: 2
Date: Fri, 7 Aug 2009 05:06:02 -0700 (PDT)
From: "Bruce D. Ray" <brucedray at yahoo.com>
Subject: Re: [gmx-users] Energy Minimisation and Equilibration
Problems
To: gmx-users at gromacs.org
Message-ID: <664136.39384.qm at web35807.mail.mud.yahoo.com>
Content-Type: text/plain; charset="us-ascii"
On Thursday, August 6, 2009 at 7:59:43 PM Nancy <nancy5villa at gmail.com>
wrote:
> I ran the minimisation, and mdrun gave the following last few lines of
output:
>
> ==================================
> Step=19990, Dmax= 7.8e-06 nm, Epot= -7.14922e+04 Fmax= 3.19585e+04, atom=
2395
> Step=19992, Dmax= 4.7e-06 nm, Epot= -7.14924e+04 Fmax= 8.72456e+03, atom=
2395
>
Step=19993, Dmax= 5.6e-06 nm, Epot= -7.14927e+04 Fmax= 3.70693e+04, atom=
2395
> Step=19994, Dmax= 6.8e-06 nm, Epot= -7.14929e+04 Fmax= 2.10513e+04, atom=
2395
> Step=19995, Dmax= 8.1e-06 nm, Epot= -7.14929e+04 Fmax= 4.71234e+04, atom=
2395
>
Step=19996, Dmax= 9.7e-06 nm, Epot= -7.14931e+04 Fmax= 3.68827e+04, atom=
2395
> Step=19998, Dmax= 5.8e-06 nm, Epot= -7.14933e+04 Fmax= 1.35461e+04, atom=
2395
> Step=19999, Dmax= 7.0e-06 nm, Epot= -7.14933e+04 Fmax= 4.77130e+04, atom=
2395
>
Step=20000, Dmax= 8.4e-06 nm, Epot= -7.14936e+04 Fmax= 2.41860e+04, atom=
2395
>
> writing lowest energy coordinates.
>
> Steepest Descents did not converge to Fmax < 10 in 20001 steps.
> Potential Energy = -7.1493609e+04
>
Maximum force = 2.4185994e+04 on atom 2395
> Norm of force = 8.1511212e+02
> ==================================
>
> As you can be seen, the forces still do not converge to Fmax < 10, even
after 20,000 steps.
>
> Does anyone know what the problem might be?
The problem is my error in the specification of non-bonded interaction
combination rules,
FudgeLJ, and FudgeQQ for gromacs force fields.
Line 7 of your file ffethanediol.itp currently reads:
1 2 yes 0.5 0.833333
This was taken from ambconv and is correct for amber and gaff force fields,
but not
for gromacs force fields, nor for OPLS-AA.
Change line 7 of the file ffethanediol.itp to read:
1 1 no 1.0 1.0
The correction is in topolbuild 1.3 which is not yet released, but this
error was not caught
for the topolbuild 1.2 series. Quite frankly, I had forgotten that
modification was made as
I've been editing the set of tables needed to add OPLS-AA to the mix of
force fields available.
As a general note. For gromacs force field topologies generated with
anything in the
topolbuild 1.2 series, this edit to the itp file that specifies the defaults
is required.
Sincerely,
--
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273
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Message: 3
Date: Fri, 07 Aug 2009 14:49:45 +0200
From: Baofu Qiao <qiaobf at gmail.com>
Subject: Re: [gmx-users] question about mdrun -append
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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