[gmx-users] Particle type 'B' in topology file?

[Justin A. Lemkul]

cdalgicdir wrote:
> Hi all,
> 
> I have performed a simulation where for an atomtype, I accidentally put 
> 'B' instead of 'A' which stands for 'atom'. The manual doesn't mention 
> any 'B''s for particle type, (it mentions A,S,V and D). I have then 
> corrected this (replaced B with A) and obtained a totally different 
> configuration. I now wonder what have I used as particle type for the 
> particle I have defined as type 'B'?
> 
> What does "B" as particle type stand for?
> 

Some sort of bonded type, per toppush.c and atoms.h, but it's not exactly clear 
what this type is.  In any case, you shouldn't be using it if atomtype Y is 
indeed an atom.  You'll get unexpected results.

-Justin

> Atomtypes section of my topology file:
> 
> [ atomtypes ]
> ;name   mass    charge  ptype   V(c6)   W(c12)
>     X          1         0.000     A        1.0       1.0
>     Y          1         0.000     B        1.0       1.0
> 
> Thanks,
> 
> Cahit

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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