[gmx-users] dummy atom definition prob in FEP

[Stéphane Téletchéa]

Wang Qin a écrit :
> Hi there,
>         I have a problems when I do a FEP calculation.
>         Below is how I defined dummy atoms in the topology file:
> [atom]
> ;nr     type            resnr   residue atom    cgnr    charge        
> mass            type_B  charge_B        mass_B
> 21      opls_172        1       LG6     H21     21      0.4650  
> 1.00800         opls_0          0.0000  0.000000
> 22      opls_172        1       LG6     H22     22      0.4650  
> 1.00800         opls_0          0.0000  0.000000
> ......
> 

I think you need to specify the mass_B=mass_A, at least this is how it 
is setup in the tutorials i've done (the one from Berk Hess and the 
other one from David Mobley).

I've also done calculations without setting the mass for B (like you 
did) and did not encounter any problem, the error you're seing could 
thus come from another part of your system.

Cheers,
Stéphane

-- 
Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901