Re: Volume Entry

From: Rawan Al Nsour (alnsourra_at_vcu.edu)
Date: Sun Feb 16 2014 - 16:36:04 CST

the system is c4f10 so the total is 14 atoms.

On Sun, Feb 16, 2014 at 4:28 PM, Aron Broom <broomsday_at_gmail.com> wrote:

> 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
>

-- 
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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