On Sat, Feb 20, 2021, Vaibhav Dixit wrote:
>I ran MD with 10, 15 and 30A TIP3PBOX to understand the effect of box size
>on relative FF energies between two systems.
>The calculations when well with 10 and 15A box size.
>But I'm getting the following error in mdout file with the system setup
>with 30A TIP3PBOX.
It looks like you set up tleap for a periodic system, but then set ntb=0
in your MD input. But it's not clear what you are trying to compute here:
do you just want a single-point energy as a function of amount of solvent?
Also, remember that tleap's solvate options only create a starting point for
further simulation. For example, the starting density is far from 1.0.
Here's one idea, if I am reading your intent correctly: run a periodic
simulation in the usual way, and get each system equilibrated to its final
temperature and density. Then use the "closest" command in cpptraj to
get various sizes of water box. For each of these, do a non-periodic
calculations (cpptraj can help you get the prmtop files), and use igb=6
to carry out the single point calculations.
...good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Feb 20 2021 - 06:30:04 PST
