Thanks for your reply. I had a read in the docs and did try few things.
Yet I still get these errors:
Command line:
gmx grompp -f SPE.mdp -c DnaAmber.pdb -p DnaAmberSB_GMX.top -o speSB.tpr
Ignoring obsolete mdp entry 'ns-type'
ERROR 1 [file SPE.mdp]:
With Verlet lists only full pbc or pbc=xy with walls is supported
ERROR 2 [file SPE.mdp]:
With Verlet lists nstlist should be larger than 0
NOTE 1 [file SPE.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
My input file is now:
# Create SPE.mdp file #single point energy
cat << EOF >| SPE.mdp
integrator = steep
nsteps = 0
dt = 0.001
constraints = none
emtol = 10.0
emstep = 0.01
nstcomm = 1
ns-type = simple
nstlist = 0
rlist = 0
rcoulomb = 0
rvdw = 0
Tcoupl = no
Pcoupl = no
gen_vel = no
nstxout = 1
pbc = no
nstlog = 1
nstenergy = 1
nstcalcenergy = 1
nstvout = 1
nstfout = 1
nstxout-compressed = 1
comm-mode = ANGULAR
continuation = yes
EOF
I’m trying with integrator = steep. I need just ONE step calculation, it does not matter if md or steep, as long as it’s just one step and then I want the energies. I don’t intend to run simulations, my aim here is just to see if my algorithm is converting systems from AMBER to GROMACS correctly.
Also, reading the docs, I don’t understand what happened with ns-type, I see Molecular dynamics parameters (.mdp options) — GROMACS 2021 documentation
and I’m strictly trying to follow what’s written there for pbc = no.
Is the manual missing something?
I also note some inconsistencies in the manual regarding ‘_’ and '-" (underscore x hyphen). For example, in GMX 4.5 and before it used to be: ns_type, comm_mode, but now it’s ns-type, comm-mode, yet gen_vel is still the same (with underscore).
And again about ns-type (or ns_type). The output command states: Ignoring obsolete mdp entry 'ns-type'; yet, the manual still mention it, though only and solely in Molecular dynamics parameters (.mdp options) — GROMACS 2021 documentation as referred before and stated here:
pbc
xyz
Use periodic boundary conditions in all directions.
no
Use no periodic boundary conditions, ignore the box. To simulate without cut-offs, set all cut-offs and
nstlist to 0. For best performance without cut-offs on a single MPI rank, set nstlist to zero and
ns-type=simple.
xy
Use periodic boundary conditions in x and y directions only. This works only with ns-type=grid and
can be used in combination with walls. Without walls or with only one wall the system size is infinite
in the z direction. Therefore pressure coupling or Ewald summation methods can not be used.
These disadvantages do not apply when two walls are used.
Nevertheless, my fear resides here: Molecular dynamics parameters (.mdp options) — GROMACS 2021 documentation when it states for nstlist = 0:
... But vacuum simulations are (temporarily) not supported.
So, if I set nstlist = 10 (again, I care only for ONE step), I got just one error:
ERROR 1 [file SPE.mdp]:
With Verlet lists only full pbc or pbc=xy with walls is supported
However, I got this enigmatic note that drives back to square one, in a catch-22 conundrum:
NOTE 1 [file SPE.mdp]:
Simulating without cut-offs can be (slightly) faster with nstlist=0,
nstype=simple and only one MPI rank
And if someone pays careful attention, one will note a ... nstype=simple ... above. But wait, wasn’t it ns_type, or ns-type or is it obsolete? (sorry, I don’t intend to be sarcastic here, I’m just very vexed with all that).
I hope this can be clarified. Any help would be very appreciated.
Best regards,
Alan