RE: [ESPResSo] Re: non-bonded interactions not showing up in theespresso polymer script for analyze energy command

[Limbach, Hans Joerg, LAUSANNE, NRC-FS]

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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