Re: [gmx-users] switching and shifting in GMX 4.6 on GPUs

> >>> >>> Hi, >>> >>> The nomenclature is confusing here. >>> I don't recall the details of the switching in CHARMM. >>> But switch in Gromacs refers to switching the potential. >>> Shift in Gromacs refers to switching the for

Re: [gmx-users] switching and shifting in GMX 4.6 on GPUs

ers to switching the force and thereby shifting the >>potential. >> >> A switch on the force only (thus "shift" in Gromacs) can usually be >>matched pretty >> well by a plain cut-off with shifted potential by choosing the cut-off >>such that either >&

Re: [gmx-users] switching and shifting in GMX 4.6 on GPUs

nergy matches for the system of interest. I expect these two cut-offs to be > very similar. > > Cheers, > > Berk > > >> Subject: Re: [gmx-users] switching and shifting in GMX 4.6 on GPUs >> From: jesoren...@ucsd.edu >> Date

RE: [gmx-users] switching and shifting in GMX 4.6 on GPUs

e very similar. Cheers, Berk ---- > Subject: Re: [gmx-users] switching and shifting in GMX 4.6 on GPUs > From: jesoren...@ucsd.edu > Date: Thu, 24 Jan 2013 14:20:09 -0800 > To: gmx-users@gromacs.org > > Hi Berk, > > I am running membrane

Re: [gmx-users] switching and shifting in GMX 4.6 on GPUs

Hi Berk, I am running membrane simulations using both the CHARMM36 and MARTINI v. 2.1 parameters. So both those cut-off treatments are important to me, but if there are ways around it I'd be happy to explore them to be able to use the GPUs. The place it would be most effective would probably be

RE: [gmx-users] switching and shifting in GMX 4.6 on GPUs

Hi, I am not a fan of especially switching the potential, as that produces artifacts. Shifting is less harmful, but unnecessary in nearly all cases. But I do realize some force fields require this (although you can probably find a cut-off setting at which results would be very similar). Another