This is 2018, I will compare later. The issue is mostly sort of solved,
as I just moved all of electrostatics to 'cut-off' with a large radius
for the rerun.
I first thought it was because the system was not neutral (ion + water
without the counterion, so it refused to report the PME part), but same
behavior with a counterion.
It would be interesting to see if you guys could independently reproduce
this with me supplying just the mdp files. Just a 3x3x3 box with a
single K+ ion and TIP4P water. em followed by 1 ns NPT (Berendsen)
relax, followed by 10 ns NPT production test.
Alex
On 4/9/2018 7:12 PM, Mark Abraham wrote:
Hi,
What version is this? What does gmx compare report amwhen comparing the two
tpr files?
Mark
On Mon, Apr 9, 2018, 22:54 Alex <nedoma...@gmail.com> wrote:
Hi all,
Something funny is happening. I have a very simple system: an ion in bulk
TIP4P water running under OPLS-AA. mdp excerpt below:
nstlist = 20
pbc = xyz
periodic_molecules = yes
ns_type = grid
rlist = 1.0
coulombtype = pme
fourierspacing = 0.135
rcoulomb = 1.0
rvdw = 1.0
vdwtype = cut-off
cutoff-scheme = Verlet
In order to determine ion-solvent interaction energy, i have a rerun mdp
that is identical to the one used for the actual simulation, but with
energygrps = K SOL
added. When applying gmx energy to the rerun edr, the only K-SOL options
are:
41 Coul-SR:K-SOL
42 LJ-SR:K-SOL
Nothing long-range. This has never been the case before and PME
contribution was always there.
Any suggestions?
Thank you,
Alex
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