Thanks James!
I was also wondering whether there is a significant penalty in performance
if I use rlist=1.2 instead of rlist=1.0
There has already been a discussion in the NAMD mailing list about the VDW
cutoff issue:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/7551.html
It is apparently common among NAMD users to use switch for VDW between 0.8
and 1.0 nm. I have often received negative criticism from supercomputer
grant reviewers whenever I suggested using a 1.0 - 1.2 switching distance
for VDW and 1.2 nm for Coulomb as in their eyes a 1.0 cutoff distance is
enough (when PME is in use).
Thanks!
Gianluca
On Sun, 25 Aug 2013, James Krieger wrote:
Here is a relevant previous discussion
http://lists.gromacs.org/pipermail/gmx-users/2013-May/081425.html
Best wishes
James
On 25 Aug 2013, at 00:28, James Krieger <jkrie...@mrc-lmb.cam.ac.uk> wrote:
CHARMM is generally used with vdw switching between 1.0 and 1.2 nm - I
presume it must be more accurate that way. There are a number of
discussions on this already. Justin recommended using rlistlong 1.4 as
well I think. You might want to use a short range cutoff (rcoulomb) of
1.2 for PME as well. That is what was done in the Bjelkmar et al paper
where CHARMM27 was implemented in GROMACS
(http://pubs.acs.org/doi/full/10.1021/ct900549r).
Best wishes
James
On 24 Aug 2013, at 23:08, Gianluca Interlandi <gianl...@u.washington.edu> wrote:
Hi!
I am running explicit solvent simulations with the CHARMM force field
implemented in gromacs 4.6.3. For VDW I have been using:
rlist = 1.0
vdw-type = Cut-off
rvdw = 1.0
in conjunction with PME and rcoulomb=1 for electrostatics.
I wonder whether it would be more accurate to use instead a switching function
for VDW between 0.8 and 1.0 and a larger rlist:
rlist = 1.2
vdw-type = Switch
rvdw_switch = 0.8
rvdw = 1.0
My question is: does switching between 0.8 and 1.0 generate less artifacts than
abrupt truncation at 1.0 nm for VDW?
Thanks!
Gianluca
-----------------------------------------------------
Gianluca Interlandi, PhD gianl...@u.washington.edu
http://artemide.bioeng.washington.edu/
Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-----------------------------------------------------
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
http://healthynaturalbaby.org
-----------------------------------------------------
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
