[ESPResSo] RE: Some notational issues:

[Christopher Jesudason]

Hi,
1) Concerning th 1/r P3M potential p. 32 , I assume
that the temperature multiplicative factor must be kT
and not T after the Bjerrum length l_b since your bond
constants are also parametrized according to kT.
2) I take it that constraint modes are not yet
available ; i.e. a chain of rigid bonds that can bend
in the dihedral plane where the bond lengths are
always constant. The constraints mentioned seem to
refer to only surfaces of interactions that is SHAKE 
and RATTLE like algorithms are of limited application.
For our work here, considerable speedup would be
achieved by constraint dynamics.
Chris 
--- "Limbach, Hans Joerg, LAUSANNE, NRC-FS"
<address@hidden> wrote:

> Dear Christopher 
> 
> Espresso returns the nonbonded energies correctly.
> The not readable comment in the UG just states that
> the different analyze energy commands should be
> documented more properly. Please check in your
> script with 
> 
> analyze mindist 0 1
> 
> what the minimal distance between your CI (type 1)
> and your DNA (type 0) is. With a box length of 300
> and randomly places particles it takes some time
> until they move towards each other. As far as I
> could see the output you where referring to is after
> the warmup which might be rather short.
> 
> For the future you can test your question more
> easily yourself with:
> 
> setmd box_l 10 10 10
> part 0 pos 1 1 1 type 0
> part 1 pos 1.5 1 1 type 1
> inter 0 1 lennard-jones 2 2 1 1 0
> analyze energy 
> 
> If this doesn't give you a nonzero energy, please
> bug me again!
> Regards,
> Hanjo
> 
> > -----Original Message-----
> > From: address@hidden 
> > [mailto:address@hidden On
> Behalf Of 
> > Christopher Jesudason
> > Sent: vendredi, 24. août 2007 15:34
> > To: Olaf Lenz
> > Cc: espresso
> > Subject: [ESPResSo] Re: non-bonded interactions
> not showing 
> > up in theespresso polymer script for analyze
> energy command 
> > 
> > Dear friends,
> >  I have a very simple single polymer electrolyte
> with species 
> > type 0 (150 of them ) all charged -1 interacting 
> with  
> > counterions type 1 all charged +1 [with harmonic
> potential 
> > type o and bending potential type  1 for this 
> polymer 
> > chain]. When I used the analyze command to get the
>  nonbonded 
> > interaction energies, where a repulsive LJ
> potential is 
> > swithced on for the 0 0 , 1 0 and 1 1  ions only
> the (0 0) 
> > energies show up , but the energy for the (1 0)
> and (0
> > 0)  non-bonded interactions of LJ type both show
> zero in both 
> > cases, which is impossible for the case of the (0
> 1 ) 
> > interactions because they have opposite charges. 
> > I looked into the manual and there is something in
> yellow on 
> > page 59 (top lhs) with comments that cannot be
> read because 
> > it  was placed outside the text margin, at least
> according to 
> > the viewer used here.
> > the snippet of the output is :
> >  all energy { energy -155.547420243 } { kinetic
> > 471.398271936 } { 0 HARMONIC 113.941433298 } { 1
> angle 0.0 } 
> > { 0  0 nonbonded 54.5179976882 } { 0  1 nonbonded
> 0.0 } { 1  
> > 1 nonbonded 0.0 } { coulomb
> > -795.405123166 0.0 -795.405123166 }
> > all total  -155.547420243
> > linindex01  -155.547420243
> > linindex11  471.398271936
> > linindex22  113.941433298
> >  kinetic 471.398271936
> >  nonbonded 00  54.5179976882
> >  nonbonded 10  0.0
> >  nonbonded 11  0.0
> > 113.941433298
> >  bonded  113.941433298
> > coulomb -795.405123166
> > Enclosed the code . I would be very pleased if you
> could give 
> > me an indication of  why this is the case. 
> > Has there been an ommision of the energies or is
> the total LJ 
> > interaction  energy put into the 0 0 interaction
> index in 
> > analyse energy command?
> > Please clarify. And thank you for your time. I
> hope I will be 
> > able to complete my research project with
> Espressso code. 
> > Could it be that the myconfig file needs to be
> activated?
> > Chis
> > Chris
> > --- Olaf Lenz <address@hidden> wrote:
> > 
> > >
> > > 
> > 
> > 
> >        
> >
>
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> > 
> 
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