[gmx-users] No cut-off
stripat1 at kent.edu
Thu Mar 24 06:38:51 CET 2011
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
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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