[gmx-users] VDW Cut-off vs Switch with CHARMM force field

[Gianluca Interlandi]

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 <jkrieger at 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 <gianluca at 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 gianluca at 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.
>>> -----------------------------------------------------
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-----------------------------------------------------
Gianluca Interlandi, PhD gianluca at 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
-----------------------------------------------------