Fabian Casteblanco wrote:
Thanks Justin. That clarified a lot. I'm having trouble simulating
the 1 molecule of gas methanol. I took the original energy minimized
molecule and I'm trying to start it off on NVT using the following
*.mdp file. I got rid of PBC (ns_type=simple) and I set
rlist=infinite. After correcting some errors, "Can not have
dispersion correction with pbc=no", (set dispcorr=no), and setting
nstlist=0 since Gromacs says simulating without cut-offs is usually
faster with nstlist=0, I now keep getting an error saying "Can not
have nstlist<=0 with twin-range interactions". Should nstlist be =0
as it says in the Gromacs manual when simulating with no cut-offs for
pbc=no? It says I can not have Ewald with pbc=no which makes sense
but I don't know what to replace it with.
A few things:
1. "rlist = infinite" is not an option. The value of rlist is a floating-point
number. To achieve infinite cutoffs, set rlist=rvdw=rcoulomb=0.
2. Don't use PME. Set "coulombtype = cutoff." There are no cutoff artifacts
here, since with rcoulomb=0, all interactions are calculated.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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