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

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jun 4 16:37:29 CEST 2012

On 5/06/2012 12:08 AM, Laurence Leherte wrote:
> 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.

IIRC GROMACS neighbour searching already identifies atoms with zero 
charge and/or LJ parameters and uses non-bonded code that does not 
compute contributions that are known to be zero. You should be able to 
see this from the differences in the flop accounting at the end of your 
.log files when you have different numbers of zero-charge atoms. If the 
total calculation times are similar, then the number of atoms for which 
time was saved was negligible. This would be normal for a peptide in a 
much larger quantity of water. You will have to judge the truth of this 
from the timing and flop breakdown at the end of the .log file.


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