Re: [gmx-users] Re:The effect of coulomb-modifier and vdw-modifier in Verlet cutoff scheme

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.

[gmx-users] The effect of coulomb-modifier and vdw-modifier in Verlet cutoff scheme

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

Re: [gmx-users] The effect of coulomb-modifier and vdw-modifier in Verlet cutoff scheme

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

Re: [gmx-users] The effect of coulomb-modifier and vdw-modifier in Verlet cutoff scheme

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

[gmx-users] Re:The effect of coulomb-modifier and vdw-modifier in Verlet cutoff scheme

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 ;