Re: [AMBER] Manually extending the size of the virtual box

From: case <>
Date: Thu, 26 Dec 2013 10:08:41 -0500

On Mon, Dec 16, 2013, Eugene Yedvabny wrote:

> Thank you for the suggestions. I've converted my solvent to TIP3P and igb=6
> works now to get rid of the virtual box constraints. Unfortunately my next
> step is to run these simulations with Amoeba forcefield, which I imagine
> would violate igb=6 requirements. On top of that, I still would like to get
> long trajectories with TIP4P-Ew rather than TIP3P.
> I am not averse to modifying Amber source to remove error conditions or
> even the virtual box. I figure modifying the box dimensions would be the
> easier approach than going through igb routines. Could you possibly point
> me to where in sander source I would find the virtual box routines and how
> to best enlarge the box / ignore escaping molecules?
> Lastly, for Amoeba simulations, should I even bother trying to run them in
> Amber? I've already reported one issue with the way Tinker writes out
> disulfide bridge multipoles, which end up breaking tinker_to_amber. If
> sander does not support gas-phase NVE with Amoeba then I'll cut my losses
> and try running the simulations in Tinker.

Sorry for the very slow reply. The problem with modifying the virtual box
dimensions is that "escaping" water molecules would quickly leave any
reasonbly-sized box, so I don't think your problem would be solved.

What I would try: (a) run a short igb=6 simualtion with a non-Amoeba potential
to see if it does what you want; (b) turn off the warning about extra points,
and turn on the Amoeba potential. Carefully check what you get vs results
from tinker.

You may well end up deciding to stick with Tinker. As you point out, Amber
was not at all designed for this sort of simulation. (I also mostly assumed
that people would want to use the Tinker water model if they were using the
Tinker protein force field, so there may be some gymnastics involved in even
setting up the mixed model you prefer.)


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Received on Thu Dec 26 2013 - 07:30:02 PST
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