AMBER Archive (2008)

Subject: Re: AMBER: Heating POL3 Box Troubles

From: Paul Johns (
Date: Wed Mar 19 2008 - 14:22:50 CDT

> Just to be sure: does your system pass the polarizable_water test? You
> might look at the example in that test, and see if you see something different
> from what you have in your files.
Yes, it seems to do fine with that.
> Also, what does a 5 step (say) minimization look like (set ntpr=1)?
The heating step gives the same errors as before, with energy going
through the roof, and a temperature of ******* for the first step
> You also might run the md simulation for 25 steps or so. Does it ever
> straighten itself out? (It looks like vmax is doing its job).
Nope, it never does. It always just quits on me.
> Can you check the masses in the prmtop file?
The masses seem fine in the prmtop file. H has a mass of 1.0800000E+00
and O has a mass of 1.60000000E+01
> Just guessing in the dark here. You might (re-)post the exact commands you
> used to create the initial prmtop and coordinate files.
xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff02pol.r1
loadAmberParams frcmod.pol3
solvatebox PL3 POL3BOX 20.0
saveamberparmpol PL3 pol3_4.prmtop pol3_4.inpcrd

If it helps, I'm basically trying to reproduce the results from Hore, D;
Walker, DS; Richmond, GL. /J. Am. Chem. Soc.,/ *130* (6), 1800 -1801,
2008. Basically, they are looking at the interface of water with
hydrophobic liquids. The create and equilibrate separate boxes of water
and a hydrophobic liquid, combine them, and then run MD on them.
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