Re: [AMBER] Interesting findings regarding water density, ntf values, and total potential energy

From: Liao <>
Date: Tue, 23 Nov 2021 14:39:36 -0600

Hi just a quick follow up, ntf=8 says in the manual that all non-bonding interactions are turned off, which seem to be impossible and not the case in fact. I think it actually means the 1-4 interactions are turned off (on top of ntf=7). If all non-bonded interactions were turned off then that’s truly pretty useless.

> On Nov 23, 2021, at 2:07 PM, David A Case <> wrote:
> On Wed, Nov 24, 2021, Liao wrote:
>> Here is the mdin file, and the program is pmemd.cuda. In the 3 scenarios,
>> ntf=1,2 or 8 is being changed. When ntf=2 or 8, shake must be turned on. If
>> ntf=1 also has SHAKE turned on, the results are identical to ntf=2.
> OK: the results look a little less strange now. As I understand it:
> ntf=1, ntc=2 is the same as ntf=2, ntc=2 (as it should be)
> ntf=1, ntc=1 is a very different model, since the water is now
> flexible. This can't really be called "TIP3P" any more, and one
> would expect all kinds of properties, including density, to be
> different
> ntf=8, ntc=2: I've never used this, and the extrememly abbreviated
> explanation in the manual of what ntf=8 means doesn't help much.
> (Does this really turn off all nonbonded interactions?) This option
> was put in for use with the debug facility in sander. From a
> brief look at the pme_force.F90 code, it looks like all forces are
> set to zero, i.e. that this is nearly useless for MD. Others may
> want to chime in here. Have you visualized what the final state
> looks like?
> As for the density you get for ntc=2, ntf=1,2: again the experience of
> the list may help here. I'm sure Amber has been used to simulation pure
> TIP3P water. Izadi et al, J Phys Chem Lett 5:3863, 2104 report a density
> of 0.980 for TIP3P water in Amber. (I've lost your original email that had
> the ntc=2,ntf=2 result.)
> TIP3P was originally parameterized with a non-bonded cutoff, so it's not
> a very good water model to use for PME simulations. An 8 Å Lennard-Jones
> cutoff is also a bit short -- you could see if increasing that a bit makes
> a difference. 50 ps is a pretty short simulation time, unless you have
> extensively equilibrated your boxes before starting these run.
> But as I said, there are "water experts" lurking here.
> ....dac
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Received on Tue Nov 23 2021 - 13:00:02 PST
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