Mark Abraham skrev 2011-03-24 06.52:
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.
Mark
In addition, depending on your system, the collective long-range
attraction from VdW interactions may not be insignificant. And since
you're simulating in vacuo, I guess you have an inhomogeneous system,
and dispersion corrdection may not be adequate. That's further reason to
have infinite VdW cut-offs too. And, as mark mentioned, the distances
are calculated anyway, so computing VdW will not add that much to your
simulation time.
Erik
On Thu, Mar 24, 2011 at 12:17 AM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@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.
Cheers,
Itamar
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.
Mark
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