[gmx-users] No cut-off
Mark.Abraham at anu.edu.au
Thu Mar 24 05:17:03 CET 2011
On 24/03/2011 1:34 PM, Itamar Kass wrote:
> Hi Swarnendu,
> grompp will return errer unless rlist=rcoulomb=rvdw=0, so you should
> stick to it.
> On 24/03/11 1:13 PM, Swarnendu Tripathi wrote:
>> Hello everybody,
>> I want to use the no cut-off option in gromacs for the electrostatic
>> interactions. In manual it says for this I need to define: pbc=no;
>> nstlist=0; ns-type=simple and rlist=rcoulomb=rvdw=0 in the .mdp file.
>> My questions are:
>> 1. If I choose rcoulomb=0 and rlist=rvdw=2.0 is that a problem? Do
>> you always recommend to use rlist=rcoulomb=rvdw=0 for no cut-off option?
>> 2. How should I choose the table-extension parameter now? Before,
>> with pbc=xyz (with cut-off) I used table-extension=rvdw+1/2*length of
>> the longest diagonal of the box (approximately). I am also using a
>> tabulated potential.
Since there is effectively no box once pbc=no, your tables need only be
as long as the longest possible interaction, plus some margin for when
the structure rearranges.
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