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.
Mark
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
