[gmx-users] Electrostatic interactions and atoms with nul charge

Laurence Leherte laurence.leherte at fundp.ac.be
Mon Jun 4 16:08:57 CEST 2012

Dear Gromacs users,

I am using the Amber99 FF in MD simulations of peptides (and proteins). 
In a first stage to the design a different charge distribution, most of 
the atomic charges were set equal to zero (i.e., all charges but the C 
and O backbone atoms).
It appeared that the calculation times observed for the original 
all-atom charges and the modified system are similar.

My question is thus the following one.  In order to save calculation 
time (and whatever the FF is), how is it possible to avoid that the 
atoms bearing a nul charge are considered in electrostatic calculations 
?  I should specify here that I want these atoms to be considered in the 
vdW non-bonding interactions.

I thank you very much in advance if you can provide me some hints.

Best regards,



Laurence Leherte
Laboratoire de Physico-Chimie Informatique
Unité de Chimie Physique Théorique et Structurale
Facultés Universitaires Notre-Dame de la Paix (University of Namur)
Rue de Bruxelles, 61
B-5000 Namur
Belgique (Belgium)

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