[gmx-users] Re: Energy conservation of rigid water models
wnoid at hec.utah.edu
wnoid at hec.utah.edu
Thu Feb 16 21:46:14 CET 2006
hello.
i'm certainly not a gromacs wizard, but i found that i had better luck for
things like this when i reduced the ft spacing to 0.08 and increased pme
order to 6. (but i think you need to make sure that you have the patched
version of pme.c for gromacs-3.3.) and of course i would agree that
running double precision will help. i hope that's helpful.
peace,
will noid
>
> Message: 2
> Date: Thu, 16 Feb 2006 20:48:10 +0200
> From: Janne Hirvi <janne.hirvi at joensuu.fi>
> Subject: [gmx-users] Re: Re: Energy conservation of rigid water models
To: gmx-users at gromacs.org
> Message-ID: <1140115690.43f4c8ead9694 at wwwmail.joensuu.fi>
> Content-Type: text/plain; charset=ISO-8859-1
>
>> Have you compiled gromacs in single precision?
>> I think double precision compilation is critical
>> for energy conservation in NVE.
>
> Yes, I have used only single precision compilation because it has been
enough
> accurate until now (NPT/NVT). Actually I just want to know if employed
time
> step of 2fs is applicable and so I think that I should use same
> compilation
> also for energy conservation simulation in NVE ensemble. Or may I prove
suitability of this long time step with double precision compilation even
> I
> have done other simulations with single precision compilation?
>
> Janne
>
>
>> 2006/2/16, Janne Hirvi <janne.hirvi at joensuu.fi>:
>> >
>> > Hello!
>> >
>> > I have read several messages about energy conservation problems and
solutions
>> > but however I am not sure if I have done something stupid. I have
used
>> > time
>> > step of 2.0fs for rigid SPC and SPC/E water models in simulations of
>> bulk
>> > water
>> > (NPT) and water droplets on frozen polymer surfaces (NVT). Everything
seemed to
>> > be just fine but when I tested energy conservation of bulk model in
>> NVE
>> > ensemble I was terrified.
>> >
>> > NVE bulk simulation of 1372 rigid SPC water molecules with 2fs time
>> step
>> > (total
>> > time 500ps) resulted in huge drift in total energy. I used same
>> parameters
>> > as
>> > for other simulations and even those aren't optimal I expected
atleast
>> > something better. Energy conservation seemed to be adequate only when
>> I
>> > used as
>> > short time step as 0.5fs.
>> >
>> >
>> > Time step (fs) Total Energy (kJ/mol) Drift
>> >
>> > 2.0 -45596.6 1235.5
>> > 1.0 -46147.5 330.974
>> > 0.5 -46331.1 <10 (not yet finished)
>> >
>> >
>> > Parameters:
>> >
>> > comm-mode = None or Linear
>> > nstlist = 5 or 10
>> > rlist = 1.2
>> > coulombtype = PME
>> > rcoulomb = 1.2
>> > vdw-type = Cut-off
>> > rvdw = 1.2
>> > fourierspacing = 0.12
>> > pme_order = 4
>> > ewald_rtol = 1e-05
>> > ewald_geometry = 3d
>> > tcoupl = No
>> > Pcoupl = No
>> >
>> >
>> > Bad energy conservation indicates that employed time step of 2.0fs is
>> too
>> > long
>> > but however other results from NPT bulk simulations are reasonable.
Moreover I
>> > think that its quite normal to use this long time step for rigid
water
>> > molecules. So I am willing to know if this large energy conservation
problems
>> > are acceptable and are they atleast "partially compensated" in NPT or
>> NVT
>> > ensemble when temperature coupling prevents heating of the system?
>> >
>> >
>> >
>> > Thanks for any help or comments!
>> >
>> > Janne
>> >
>> >
>> >
> ------------------------------------------------------------------------------
>> > Janne Hirvi, MSc(Physical Chemistry), Researcher
>> > University of Joensuu, Department of Chemistry, P.O.Box 111 80101
>> Joensuu,
>> > FI
>> > Tel: +358 13 2514544 & +358 50 3474223
>> > E-mail: Janne.Hirvi at joensuu.fi & hirvi at cc.joensuu.fi
>> >
>> >
> ------------------------------------------------------------------------------
>
>
>
>
> Message: 4
> Date: Thu, 16 Feb 2006 20:07:37 +0100
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Re: Re: Energy conservation of rigid water
> models
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <43F4CD79.7050302 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Janne Hirvi wrote:
>>>Have you compiled gromacs in single precision?
>>>I think double precision compilation is critical
>>>for energy conservation in NVE.
>> Yes, I have used only single precision compilation because it has been
enough
>> accurate until now (NPT/NVT). Actually I just want to know if employed
time
>> step of 2fs is applicable and so I think that I should use same
compilation
>> also for energy conservation simulation in NVE ensemble. Or may I prove
suitability of this long time step with double precision compilation even I
>> have done other simulations with single precision compilation?
>
> It is important to realize that you need this kind of precision only in
special cases, for instance when you want to derive properties from the
fluctuations of T, P, E.
>
> The algorithms in GROMACS are not perfect, that is, there are better
algroithms for integrators etc. We are working on these things.
>
> However, what is implemented, i.e. leap-frog, when used carefully, does
conserve energy. Things that spoil energy conservation are:
>
> - T coupling
> - P coupling
> - Cut-offs (both LJ and Coulomb)
> - Constraints (but not SETTLE as used for water)
> - Long time steps (in relation to the fastest vibrations)
> - Too long intervals between neighborsearching
> - To some extent, single precision (due to the fact that you sometimes
add small forces to large one, and by this lose precision).
>
>
> --
> David.
> ________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept.
of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 16 Feb 2006 20:08:06 +0000
> From: milton sonoda <mtsonoda at gmail.com>
> Subject: Re: [gmx-users] Re: Re: Energy conservation of rigid water
> models
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <271f13720602161208mab699a5j at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> I strongly sugest you to try double precision compilation
> for energy conservation in NVE.
>
> Single precision is enough for NPT/NVT due to
> convenient algorithms (velocity and volume reescaling)
> that keeps the system at the desired termodynamic state
> (constante pressure and constante temperature) masking
> the truncation errors of the single precision simulation.
>
> In NVE no algorithm is used, so the double precision
> is necessary to prevent/postpone energy drift due to
> this error acumulation.
>
>
> 2006/2/16, Janne Hirvi <janne.hirvi at joensuu.fi>:
>> > Have you compiled gromacs in single precision?
>> > I think double precision compilation is critical
>> > for energy conservation in NVE.
>> Yes, I have used only single precision compilation because it has been
enough
>> accurate until now (NPT/NVT). Actually I just want to know if employed
time
>> step of 2fs is applicable and so I think that I should use same
compilation
>> also for energy conservation simulation in NVE ensemble. Or may I prove
suitability of this long time step with double precision compilation even
>> I
>> have done other simulations with single precision compilation?
>> Janne
>> > 2006/2/16, Janne Hirvi <janne.hirvi at joensuu.fi>:
>> > >
>> > > Hello!
>> > >
>> > > I have read several messages about energy conservation problems and
solutions
>> > > but however I am not sure if I have done something stupid. I have
>> used
>> > > time
>> > > step of 2.0fs for rigid SPC and SPC/E water models in simulations
of
>> bulk
>> > > water
>> > > (NPT) and water droplets on frozen polymer surfaces (NVT).
>> Everything
>> > > seemed to
>> > > be just fine but when I tested energy conservation of bulk model in
>> NVE
>> > > ensemble I was terrified.
>> > >
>> > > NVE bulk simulation of 1372 rigid SPC water molecules with 2fs time
>> step
>> > > (total
>> > > time 500ps) resulted in huge drift in total energy. I used same
>> parameters
>> > > as
>> > > for other simulations and even those aren't optimal I expected
>> atleast
>> > > something better. Energy conservation seemed to be adequate only
>> when
>> I
>> > > used as
>> > > short time step as 0.5fs.
>> > >
>> > >
>> > > Time step (fs) Total Energy (kJ/mol) Drift
>> > >
>> > > 2.0 -45596.6 1235.5
>> > > 1.0 -46147.5 330.974
>> > > 0.5 -46331.1 <10 (not yet
>> finished)
>> > >
>> > >
>> > > Parameters:
>> > >
>> > > comm-mode = None or Linear
>> > > nstlist = 5 or 10
>> > > rlist = 1.2
>> > > coulombtype = PME
>> > > rcoulomb = 1.2
>> > > vdw-type = Cut-off
>> > > rvdw = 1.2
>> > > fourierspacing = 0.12
>> > > pme_order = 4
>> > > ewald_rtol = 1e-05
>> > > ewald_geometry = 3d
>> > > tcoupl = No
>> > > Pcoupl = No
>> > >
>> > >
>> > > Bad energy conservation indicates that employed time step of 2.0fs
>> is
>> too
>> > > long
>> > > but however other results from NPT bulk simulations are reasonable.
Moreover I
>> > > think that its quite normal to use this long time step for rigid
>> water
>> > > molecules. So I am willing to know if this large energy
conservation
>> > > problems
>> > > are acceptable and are they atleast "partially compensated" in NPT
>> or
>> NVT
>> > > ensemble when temperature coupling prevents heating of the system?
>> > >
>> > >
>> > >
>> > > Thanks for any help or comments!
>> > >
>> > > Janne
>> > >
>> > >
>> > >
>> >
>> ------------------------------------------------------------------------------
>> > > Janne Hirvi, MSc(Physical Chemistry), Researcher
>> > > University of Joensuu, Department of Chemistry, P.O.Box 111 80101
>> Joensuu,
>> > > FI
>> > > Tel: +358 13 2514544 & +358 50 3474223
>> > > E-mail: Janne.Hirvi at joensuu.fi & hirvi at cc.joensuu.fi
>> > >
>> > >
>> >
>> g
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