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

**Date:** Sun Feb 16 2014 - 15:28:27 CST

**Next message:**Tanner, John J.: "FAD topology and parameters"**Previous message:**Rawan Al Nsour: "Re: Volume Entry"**In reply to:**Rawan Al Nsour: "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 ]

yeah but the density of what? How many molecules are in your simulation?

Like Axel says, you've provided very little real information throughout

your whole series of questions. At the moment, if I was forced to guess,

it seems like you are running a simulation of one or at most two molecules

and trying to get bulk properties from that, which doesn't make sense to me.

On Sun, Feb 16, 2014 at 4:16 PM, Rawan Al Nsour <alnsourra_at_vcu.edu> wrote:

*> I am just trying to find the density from simulations, i generated a new
*

*> set of force fields parameters and I am trying to test the density and heat
*

*> of vaporization for small oligomers
*

*>
*

*>
*

*> On Sun, Feb 16, 2014 at 2:57 PM, Aron Broom <broomsday_at_gmail.com> wrote:
*

*>
*

*>> 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
*

*>>
*

*>
*

*>
*

*>
*

*> --
*

*> 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
*

*>
*

*>
*

*>
*

*>
*

*>
*

*>
*

*>
*

*>
*

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

**Next message:**Tanner, John J.: "FAD topology and parameters"**Previous message:**Rawan Al Nsour: "Re: Volume Entry"**In reply to:**Rawan Al Nsour: "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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