[gmx-users] confusion about rlist continues in 3.2

[David van der Spoel]

On Thu, 2004-01-29 at 14:55, Michael Brunsteiner wrote:
> dear gmx-users,
> 
> in gromcas-3.2 source (kernel/readir.c) it says:
> 
>   /* Allow rlist>rcoulomb for tabulated long range stuff. This just
>    * means the interaction is zero outside rcoulomb, but it helps to
>    * provide accurate energy conservation.
>    */
> 
> sounds reasonble to me (this was missing in 3.1.4), however
> further down in readir.c (as shown below) we find that rcoulomb 
> is again required to be larger than rlist, if one uses cutoff (and 
> not shift) ... why ?
> doesn't make sense to me ... sounds as if the cutoff for the
> electrostatic interactions (rcoulomb) is now greater than
> the cut-off used for creating the neighbor-list (rlist) ...
> In previous mails in this list it was said that the cut-off
> used for making the neighbour-list is actually larger than
> rlist but I don't see this "buffer-distance" anywhere in the 
> code ...
The buffer distance does not make sense for cut-off or RF, as there the
short-range cut-off is rlist. Maybe eelPME should be added to the first
if statement below:


> 
>   if ((ir->coulombtype == eelSHIFT) || (ir->coulombtype == eelSWITCH))
> {
>     sprintf(err_buf,"With coulombtype = %s rcoulomb_switch must be <
> rcoulomb",
>             eel_names[ir->coulombtype]);
>     CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
>     if (ir->rcoulomb_switch > ir->rcoulomb-0.0999) { 
>       sprintf(warn_buf,"rcoulomb should be 0.1 to 0.3 nm larger than
> rcoulomb_switch to account for diffusion and the size of charge
> groups");
>  
>       warning(NULL);
>     }
>   } else if(ir->coulombtype == eelCUT || ir->coulombtype == eelRF) {
>     sprintf(err_buf,"With coulombtype = %s, rcoulomb must be >=
> rlist",eel_names[ir->coulombtype]);
>     CHECK(ir->rlist > ir->rcoulomb);
>   }
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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