[AMBER] Non-PBC simulation in a droplet made of organic solvent

From: Veronika Jurásková <veronika.juraskova.email.cz>
Date: Mon, 22 Jan 2018 11:13:49 +0100 (CET)

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


  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,


  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,

AMBER mailing list
Received on Mon Jan 22 2018 - 02:30:02 PST
Custom Search