You don't turn on those modifiers, you choose to shift the potential. (In
the future there might be more options.) Shifting the potential is quite
different from the action of vdwtype=shift, see manual 4.1, 7.3. The
potential should be the integral of the force, if you want it to mean
anything.
Hi All,
In GROMACS 4.6.x series, Verlet cutoff scheme is introduced to enable
OpenMP parallelization and GPU acceleration. Then some new run parameters
are introduced to control the use of Verlet cutoff scheme. However, I
noticed the GROMACS manual doesn't give in-depth knowledge on some
Those modifiers shift only the potential, as manual 7.3 points out. So the
forces and sampling are unaffected, so it does not surprise me that APL is
unaffected by the use of such a shift. If your group cutoff scheme was
unbuffered (rlist = max(rcoulcomb,rvdw) and nstlist 1), then if the
observed
If one is using the potential for something (e.g. reweighting, replica
exchange) then now the possibility of a systematic deviation with shifted
potentials is real.
Mark
On Thu, May 23, 2013 at 10:11 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
Those modifiers shift only the potential, as
Dear Mark,
Could you elaborate on your answer? In my group cutoff scheme, I used
ns_type = grid ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist = 1.3 ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.3 ;
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