[gmx-users] No cut-off
stripat1 at kent.edu
Thu Mar 24 13:32:26 CET 2011
Thank you very much. Really very helpful comments.
On Thu, Mar 24, 2011 at 1:52 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> 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
> 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>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 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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