[gmx-users] No cut-off
Mark.Abraham at anu.edu.au
Thu Mar 24 06:52:06 CET 2011
On 24/03/2011 4:38 PM, Swarnendu Tripathi wrote:
> Hi all,
> Thank you for the reply. The answer I got for the second question
> about table-extension, I understand and agree with that.
> Regarding my first question I asked, I did not get any error with
> grompp even when I tried rlist=rvdw=2.0 and rcoulomb=0. For this I
> used the no cut-off conditions which I have mentioned below in my
> previous e-mail. I am using Gromacs-4.0.7. Any further suggestions or
> comments will be very helpful.
VDW interactions normally become insignificant much faster than Coulomb
interactions, so treating all Coulomb interactions and only some VDW
interactions is logical. However, performing the search for neighbours
takes time, and given that you are computing the distances already for
their Coulomb interaction, it is probably cheaper just to compute all
the VDW interactions, i.e. rlist=rvdw=0. This might be different if you
had a lot of atoms that had zero partial charge.
> On Thu, Mar 24, 2011 at 12:17 AM, Mark Abraham
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
> 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
> 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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