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

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 2 14:17:06 CET 2011

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.


> 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


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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