[gmx-users] NS in PME

Janne Hirvi janne.hirvi at joensuu.fi
Thu Apr 20 10:39:48 CEST 2006

Hello Berk and David!

Could you explain why we shouldnt use rlist>rcoulomb with PME. To my knowledge
good energy conservation will be achieved "only" with this combination because
diffusion between successive NS will be taken into account. Michael Shirts
agreed with this on gmx-developers mailing list:


but atleast I didnt understand from Berks response the fundamental basis for the
restriction to rlist=rcoulomb.

Manual of Amber8 also recommends use of larger NS cut-off than real space
cut-off with PME so that energy conservation will be achieved:

NBFLAG: If nbflag = 0, construct the direct sum nonbonded list in the "old" way,
i.e. update the list every nsnb steps. If nbflag = 1 (the default when imin = 0
or ntb > 0), nsnb is ignored, and the list is updated whenever any atom has
moved more than 1/2 skinnb since the last list update.

SKINNB: Width of the nonbonded "skin". The direct sum nonbonded list is extended
to cut + skinnb, and the van der Waals and direct electrostatic interactions
truncated at cut. Default is 2.0 Å. Use of this parameter is required for
energy conservation, and recommended for all PME runs.

Thanks for any comments in advance! 


Janne Hirvi, MSc(Physical Chemistry), Researcher
University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI
Tel: +358 13 2514544 & +358 50 3474223
E-mail: Janne.Hirvi at joensuu.fi & hirvi at cc.joensuu.fi

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