Re: Volume Entry

From: Rawan Al Nsour (alnsourra_at_vcu.edu)
Date: Sun Feb 16 2014 - 15:16:44 CST

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

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