Dear Amber list,
I am trying to run QM/MM simulation of small organic molecule in organic
solvent (THF) using electronic embedding. I would like to use non-PBC
simulation in a droplet. I prepared the system (organic molecule + 999 THF),
minimized it and heated it to 298 K. Then, I run NVT simulation (only MM in
Amber) to let the system relax for 100 ps before the QM/MM simulation.
Because the droplet in a vacuum is a little unphysical, I tried to use
solvent cap to avoid evaporation into vacuum. I had the cap defined in my
prompt file, therefore I added
ivcap = 0, fcap = 10,
into my input file:
NVT relaxing 100 ps
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 0,
cut = 100.0, ntr = 1,
ntc = 1, ntf = 1,
tempi = 298.15, temp0 = 298.15,
ntt = 3, gamma_ln = 1.0,
restraint_wt = 500,
restraintmask=.1-26,
nstlim = 200000, dt = 0.0005
ivcap=0, fcap = 10,
ntpr = 50, ntwx = 50, ntwr = 50
/
Unfortunately, I am afraid it didn't work. My simulation crashed after cca
50 ps with the following error
Frac coord min, max: 4.130905485925260E-002 1.00004639879087
The system has extended beyond
the extent of the virtual box.
Restarting sander will recalculate
a new virtual box with 30 Angstroms
extra on each side, if there is a
restart file for this configuration.
SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
Atom out of bounds. If a restart has been written,
restarting should resolve the error
When I checked the trajectory in VMD, there were some THF molecules
evaporating from the sphere. Therefore, I tried to run the same simulation
with higher fcap but with the same results.
I would like to ask whether the cap tool can be used with a different
solvent than water. If yes - how can I set the cap correctly? If not - is
there any other option how to avoid evaporation of THF?
Thank you for the reply,
Veronika
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Received on Mon Jan 22 2018 - 02:30:02 PST
