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:
http://www.gromacs.org/pipermail/gmx-developers/2006-April/001581.html 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 are 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 ------------------------------------------------------------------------------ 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: [EMAIL PROTECTED] & [EMAIL PROTECTED] ------------------------------------------------------------------------------ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
