**From:** Aron Broom (*broomsday_at_gmail.com*)

**Date:** Sun Feb 16 2014 - 13:57:33 CST

**Next message:**Maryam Sayadi: "Instability in thermodynamic integration"**Previous message:**Axel Kohlmeyer: "Re: Volume Entry"**In reply to:**Axel Kohlmeyer: "Re: Volume Entry"**Next in thread:**Rawan Al Nsour: "Re: Volume Entry"**Reply:**Rawan Al Nsour: "Re: Volume Entry"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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

**Next message:**Maryam Sayadi: "Instability in thermodynamic integration"**Previous message:**Axel Kohlmeyer: "Re: Volume Entry"**In reply to:**Axel Kohlmeyer: "Re: Volume Entry"**Next in thread:**Rawan Al Nsour: "Re: Volume Entry"**Reply:**Rawan Al Nsour: "Re: Volume Entry"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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