Re: Volume Entry

From: Aron Broom (broomsday_at_gmail.com)
Date: Sun Feb 16 2014 - 13:57:33 CST

in particular, are you hoping to reproduce the properties of a bulk
solution of your molecule by making a periodic cell from just ONE molecule?
 If so, there are problems beyond the computational one of the small cell
size.

On Sun, Feb 16, 2014 at 2:51 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> this doesn't help a lot, either. you don't explain what you want to do
> with this simulation, what your overall intentions are, how you got
> where you are, where the error is coming from, and there are still
> files missing to reproduce your simulation. nobody here can read your
> mind and an input file only tells part of the story.
>
> axel.
>
>
>
> On Sun, Feb 16, 2014 at 2:08 PM, Rawan Al Nsour <alnsourra_at_vcu.edu> wrote:
> > the conf file is
> > structure c6ptfe.psf
> > coordinates c6ptfe.pdb
> > outputName npt-01
> >
> > set temperature 298
> >
> > firsttimestep 0
> >
> > # Input
> > paraTypeCharmm on
> > parameters par_all27_prot_lipid.inp
> >
> > # NOTE: Do not set the initial velocity temperature if you
> > # have also specified a .vel restart file!
> > temperature $temperature
> >
> >
> > # Periodic Boundary Conditions
> > # NOTE: Do not set the periodic cell basis if you have also
> > # specified an .xsc restart file!
> > if {1} {
> > cellBasisVector1 6.3 0. 0.
> > cellBasisVector2 0. 8.54 0.
> > cellBasisVector3 0. 0. 6.3
> > cellOrigin 0.0 0.0 0.0
> > }
> >
> > wrapAll on
> >
> >
> > # Force-Field Parameters
> > exclude scaled1-4
> > 1-4scaling 1.0
> > cutoff 7.0
> > switching on
> > switchdist 5.0
> > pairlistdist 8.5
> > margin 2.5
> > vdwGeometricSigma yes
> >
> >
> > # Integrator Parameters
> > timestep 0.5 ;# 1fs/step
> > rigidBonds none ;# needed for 1fs steps
> > nonbondedFreq 1
> > fullElectFrequency 2
> > stepspercycle 20
> >
> >
> > #PME (for full-system periodic electrostatics)
> > if {1} {
> > PME yes
> > PMEGridSpacing 0.5
> > }
> >
> >
> > # Constant Temperature Control
> > langevin on ;# do langevin dynamics
> > langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
> > langevinTemp $temperature
> >
> > # Constant Pressure Control (variable volume)
> > if {1} {
> > useGroupPressure yes ;# needed for 2fs steps
> > useFlexibleCell no ;# no for water box, yes for membrane
> > useConstantArea no ;# no for water box, yes for membrane
> >
> > langevinPiston on
> > langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> > langevinPistonPeriod 200.0
> > langevinPistonDecay 50.0
> > langevinPistonTemp $temperature
> > }
> >
> >
> > restartfreq 50 ;
> > dcdfreq 25
> > xstFreq 25
> > outputEnergies 10
> > outputPressure 10
> >
> > minimize 100
> >
> > run 250000 ;# .9ns
> >
> >
> > On Sun, Feb 16, 2014 at 11:38 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> >>
> >> On Sun, Feb 16, 2014 at 11:29 AM, Rawan Al Nsour <alnsourra_at_vcu.edu>
> >> wrote:
> >> > Dr. Axel,
> >> > I got the C4F10 experimental density, then I built the box volume
> based
> >> > on
> >> > that value. unfortunately, I got the message " the cell is too small"
> >>
> >> there is far too little information in this one sentence to give any
> >> kind of meaningful advice.
> >>
> >>
> >> >
> >> > On Mon, Feb 10, 2014 at 12:09 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> >> > wrote:
> >> >>
> >> >> On Mon, Feb 10, 2014 at 12:04 PM, Rawan Al Nsour <alnsourra_at_vcu.edu>
> >> >> wrote:
> >> >> > First, many thanks for you sir for taking the time to reply.
> >> >> > what I want to do is to find the density for small fluorocarbons
> such
> >> >> > as
> >> >> > c6f14, but it is very small molecule
> >> >>
> >> >> so what?
> >> >>
> >> >> please read my answer again, think about it for a bit and hopefully
> >> >> you'll figure out where you are going in the wrong direction.
> >> >>
> >> >> axel.
> >> >>
> >> >> > On Mon, Feb 10, 2014 at 11:45 AM, Axel Kohlmeyer <
> akohlmey_at_gmail.com>
> >> >> > wrote:
> >> >> >>
> >> >> >> please always copy the mailing list on your responses, so the
> >> >> >> discussion gets properly archived and people can later look up the
> >> >> >> outcome (and save time by not having to ask the same question).
> >> >> >>
> >> >> >> On Mon, Feb 10, 2014 at 11:25 AM, Rawan Al Nsour <
> alnsourra_at_vcu.edu>
> >> >> >> wrote:
> >> >> >> > Do you mean they are Zero
> >> >> >>
> >> >> >> or at best ill-defined.
> >> >> >>
> >> >> >> > then how can I find c6f14 density
> >> >> >>
> >> >> >> now *that* is a different question. density is computed from the
> >> >> >> total
> >> >> >> mass in a reference volume. while it may be difficult to define
> the
> >> >> >> reference volume for a single molecule, it is rather
> straightforward
> >> >> >> to do so for a bulk system, provided you have a homogeneous
> >> >> >> distribution of the density (at least at the scale and level of
> >> >> >> accuracy that you are looking at). if you do not have a bulk
> system,
> >> >> >> like in the case you are describing, you have to determine a
> >> >> >> suitable
> >> >> >> reference volume yourself (e.g. through 3d-binning) and can try to
> >> >> >> compute the density for this/these references through averaging.
> >> >> >>
> >> >> >> in short, you have to properly define what you are computing,
> >> >> >> because
> >> >> >> what you are asking for is not well defined.
> >> >> >>
> >> >> >> axel.
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> > On Mon, Feb 10, 2014 at 11:12 AM, Axel Kohlmeyer
> >> >> >> > <akohlmey_at_gmail.com>
> >> >> >> > wrote:
> >> >> >> >>
> >> >> >> >> On Mon, Feb 10, 2014 at 11:08 AM, Rawan Al Nsour
> >> >> >> >> <alnsourra_at_vcu.edu>
> >> >> >> >> wrote:
> >> >> >> >> > I simulated a small molecule c6f14 without (PBC's and PME), I
> >> >> >> >> > did
> >> >> >> >> > not
> >> >> >> >> > see
> >> >> >> >> > the volume entry in the output file, how can I measure the
> >> >> >> >> > volume?
> >> >> >> >>
> >> >> >> >> counter question: what is the volume of a point particle?
> >> >> >> >>
> >> >> >> >> bonus question: what is the volume of a collection of point
> >> >> >> >> particles?
> >> >> >> >>
> >> >> >> >> axel.
> >> >> >> >>
> >> >> >> >> > Thanks
> >> >> >> >> >
> >> >> >> >> > --
> >> >> >> >> > Rawan Al Nsour
> >> >> >> >> > Ph.D. Candidate
> >> >> >> >> > Department of Mechanical and Nuclear Engineering
> >> >> >> >> > School of Engineering, Virginia Commonwealth University
> >> >> >> >> > E-mail: alnsourra_at_vcu.edu
> >> >> >> >> > 401 W. Main Street, Room E3216
> >> >> >> >> > P.O. Box 843015
> >> >> >> >> > Richmond, Virginia 23284-3015
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >>
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> --
> >> >> >> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >> >> >> >> College of Science & Technology, Temple University,
> Philadelphia
> >> >> >> >> PA,
> >> >> >> >> USA
> >> >> >> >> International Centre for Theoretical Physics, Trieste. Italy.
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> > --
> >> >> >> > Rawan Al Nsour
> >> >> >> > Ph.D. Candidate
> >> >> >> > Department of Mechanical and Nuclear Engineering
> >> >> >> > School of Engineering, Virginia Commonwealth University
> >> >> >> > E-mail: alnsourra_at_vcu.edu
> >> >> >> > 401 W. Main Street, Room E3216
> >> >> >> > P.O. Box 843015
> >> >> >> > Richmond, Virginia 23284-3015
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >> >> >> College of Science & Technology, Temple University, Philadelphia
> PA,
> >> >> >> USA
> >> >> >> International Centre for Theoretical Physics, Trieste. Italy.
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> > --
> >> >> > Rawan Al Nsour
> >> >> > Ph.D. Candidate
> >> >> > Department of Mechanical and Nuclear Engineering
> >> >> > School of Engineering, Virginia Commonwealth University
> >> >> > E-mail: alnsourra_at_vcu.edu
> >> >> > 401 W. Main Street, Room E3216
> >> >> > P.O. Box 843015
> >> >> > Richmond, Virginia 23284-3015
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >> >> College of Science & Technology, Temple University, Philadelphia PA,
> >> >> USA
> >> >> International Centre for Theoretical Physics, Trieste. Italy.
> >> >
> >> >
> >> >
> >> >
> >> > --
> >> > Rawan Al Nsour
> >> > Ph.D. Candidate
> >> > Department of Mechanical and Nuclear Engineering
> >> > School of Engineering, Virginia Commonwealth University
> >> > E-mail: alnsourra_at_vcu.edu
> >> > 401 W. Main Street, Room E3216
> >> > P.O. Box 843015
> >> > Richmond, Virginia 23284-3015
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >> College of Science & Technology, Temple University, Philadelphia PA, USA
> >> International Centre for Theoretical Physics, Trieste. Italy.
> >
> >
> >
> >
> > --
> > Rawan Al Nsour
> > Ph.D. Candidate
> > Department of Mechanical and Nuclear Engineering
> > School of Engineering, Virginia Commonwealth University
> > E-mail: alnsourra_at_vcu.edu
> > 401 W. Main Street, Room E3216
> > P.O. Box 843015
> > Richmond, Virginia 23284-3015
> >
> >
> >
> >
> >
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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