RE: [gmx-users] Free energy calculations and speed problems

Hi, Note that there are proper options for this (no cut-off's): ns_type = simple pbc = none nstlist = 0 rlist = 0 rcoulomb = 0 rvdw = 0 Berk. > Date: Tue, 20 May 2008 12:45:35 -0700 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Free energy

Re: [gmx-users] Free energy calculations and speed problems

Justin and Michael, Just to clarify here, I don't think you want the "long cutoff in vacuum" scheme to give you the same results as the "PME in vacuum" scheme. That is, if you use PME in vacuum with a periodic box, you will be including copies of the long-range unscreened electrostatic interaction

Re: [gmx-users] Free energy calculations and speed problems

Just to follow up - the cutoff scheme worked quite well. It gave me energies that were ~1% different from those of the PME calculation, which I think compares quite well. The 10-ps run I attempted now takes 3 seconds, instead of 20 minutes. Thanks to everyone for the suggestions. -Justin Quot

Re: [gmx-users] Free energy calculations and speed problems

Thanks to everyone for the insights. I'll try running things with the cutoff and see how it goes. -Justin Quoting Michael Shirts <[EMAIL PROTECTED]>: > Hi, Justin- > > Have you considered -not- running PME in vacuo? If you set your > cutoffs and rlist large enough, then you can just run with

Re: [gmx-users] Free energy calculations and speed problems

Hi, Justin- Have you considered -not- running PME in vacuo? If you set your cutoffs and rlist large enough, then you can just run with simple cutoffs, and it should run -fst-. Of course, you should compare to the energy with PME -- if they are not equivalent, then you many need to go back an

Re: [gmx-users] Free energy calculations and speed problems

Yes, what he said. On Mon, May 19, 2008 at 3:00 PM, van Bemmelen <[EMAIL PROTECTED]> wrote: > Hi Justin, > > You shouldn't use PME in vacuo. Just use pbc=no and infinite (i.o.w.: no) > cutoffs. > > I'm not entirely sure why PME takes such a long time, but I can give a very > wild guess. It may hav

RE: [gmx-users] Free energy calculations and speed problems

Hi Justin, You shouldn't use PME in vacuo. Just use pbc=no and infinite (i.o.w.: no) cutoffs. I'm not entirely sure why PME takes such a long time, but I can give a very wild guess. It may have something to do with the fact that, if I remember correctly, the Fourier transform of one (or a few)