Dear Professor Shirts, Thank you so much. I really appreciate your time in responding to my post and providing advice. I will try your suggested parameters for reasonably good energy conservation, and I will let you know how it goes.
Thanks again for your time. I will be in touch. Andrew ------------------------------ Date: Wed, 10 Aug 2011 17:50:13 -0400 From: Michael Shirts <michael.shi...@virginia.edu> Subject: Re: [gmx-users] Recommended parameters for NVE simulation of SPCE water > 1. NOTE 1 above suggests that I use vdwtype = Shift. When I do this, do > you recommend that I apply long range dispersion corrections for both energy > and pressure, using DispCorr = EnerPres, or for only energy, using DispCorr > = Ener? Typically, for various (non-NVE) calculations, I have been using > DispCorr = no, but I am not sure if this is a good idea. Pages 97-98 of the > Gromacs 4.5.4 manual seem to suggest that the energy correction due to > DispCorr is small and usually only significant for free energy calculations > (which I will not be doing here). As a rule of thumb, do you typically turn > dispersion corrections off? For constant pressure simulations, or for reaching the constant pressure equilibrium simulation, you should definitely include a dispersion correction -- the density will be too large, and will be cutoff dependent. For constant volume simulations, the dispersion correction will be constant. It will thus NOT affect energy conservation, but WILL affect average potential energy and average total energy, significantly. > 2. NOTE 2 above suggests that I use either coulombtype = PME-Switch or > coulombtype = Reaction-Field-zero. Do you have any advice or > recommendation? For pretty good energy conservation, I would suggest: rlist = 1.3 coulombtype = PME rcoulomb = 1.1 vdw-type = Switch rvdw-switch = 1.0 rvdw = 1.1 This should work quite well -- you might get some drift after 1-2 ns, but not much. I'm working on developing suggested PME parameters right now for highly quantitative work, but it's not quite ready yet. ~~~~~~~~~~~~ Michael Shirts Assistant Professor Department of Chemical Engineering University of Virginia michael.shi...@virginia.edu (434)-243-1821 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists