Re: amber-developers: fixup to max14

From: Lachele Foley <>
Date: Wed, 12 Nov 2008 19:00:36 -0500

> 1. Why are you doing lots of minimization in the first place?

Because I was taught that it is always safest to minimize a
structure before attempting a simulation. I think the idea
is to prevent unexpected behaviors related to starting with
a high-energy or highly-ordered system, etc.

> (with explicit solvent) is to only do minimization if the starting structure
> is so bad that MD will fail. 14,000 cycles seems way beyond what is
> necessary or productive.

Dad used to call me a perfectionist... It's because the curve gets
really flat there. I can stamp on the OCD a little if necessary.

> 2. Related: why do ntb=0 if you have explicit solvent?

Because using ntb=1 gave me a box that was 1/3 empty, right
down the middle, and that caused the first n tries at a CP
run to fail because the CV heating didn't help at all.

I am considering trying to heat directly from the leap-generated,
perfect-array structure, but am concerned about getting results
like those mentioned in my answer to [1]. And, in a purely
aesthetic sense, I find it odd to "heat" from a structure that
really can't be stable at anything other than a very high energy,
and even then only fleetingly. But, I can get over that easily
enough if necessary.

> 3. If I read correctly, you are starting with a very low density
> of water (0.6 g/cm3)?

Not on purpose! That's what leap made when I solvated the box. I
was just wondering if that was a bug or a feature. It isn't that the
solvent is hard to pack around, because I tried solvating a water
molecule, which should pack perfectly, and got 0.6 g/cc. (and after
I wrote this, I saw what you said below... but this is the answer...)

> ... What you want to do is to get going with MD, get ...

Yeah... I guess something like that will behave. I just didn't
expect it to. The manual recommends "heating" (this really high-energy
structure) at CV, but I wonder if I couldn't just set the desired
temperature and let CP adjust the density.

I did get a simulation to run long enough to have the CP adjust
the density to something reasonable. I'll check out the structure,
but when I looked halfway through, it still looked good. So, I
can just use that restart for future starting structures.

> 4. You seem not to be using pmemd. Of course, this is good in that it may
> expose sander bugs, but Bob's code is a lot less likely to have weird
> corners
> that mysteriously hang, and it will almost always be faster to boot. After
> we
> twisted his arm to get extra points into pmemd, we should take advantage of
> it.

Oh... sorry. Yes. I'll do that. Tomorrow. I hope. Thanks, Bob! I was
only slow because the prepared configs are all for admittedly faster but
proprietary compilers, and it might take a while for me to tweak it for the
compiler I have (gfortran is likely).

> (a) use the option closeness parameter (say set to 0.7) to get a little more
> reasonable initial density;

Ah... thanks.
> (b) we eventually need a TIP5PBOX setup (rather than just solvating with
> TP5).

Is that difficult to do? I think I thought that's what was happening, so I
didn't even look for an option to pack things tighter.
> I hope this all works--I want to find out what sucrose does with TIP5P and
> the corresponding glycam potentials!

I did get a simulation to run long enough to have the CP adjust
the density to something reasonable. It took about 13,000 steps
to do it. I've only got about .97 ns of (what is probably) decent
data now. Want it? How much? I can't do much with it for a few
days. I'll be running a longer simulation in the meantime.

:-) Lachele
B. Lachele Foley, PhD '92,'02
Assistant Research Scientist
Complex Carbohydrate Research Center, UGA
Received on Fri Dec 05 2008 - 14:36:13 PST
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