From: Rawan Al Nsour (alnsourra_at_vcu.edu)
Date: Sun Feb 16 2014 - 13:08:05 CST
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
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:20:29 CST