AMBER Archive (2004)

Subject: Re: AMBER: NVE&polarizable force field

From: Byungchan Kim (bk385_at_columbia.edu)
Date: Tue Feb 03 2004 - 11:54:55 CST

Hi!

Why don't you do following to make sure other factors do not affect your
simulation.

1. more conservative parameter for ewald.
You can increase grid points and assignment type. Polarizable force field
may need more accurate electrostatic interactions.

2. smaller tolerance for constraints of POL3
Because POL3 was parameterized in certain fixed geometry, I think you need
more accurate tolerance.

3. smaller tolerance for induced dipoles in case of interative solution.
Manual recommends you use 10E-7.

4. smaller timestep

Thank you

Byungchan Kim

On Mon, 2 Feb 2004, Martina Roeselova wrote:

> Thanks everyone for your help. Now, when I knew what I was looking for,
> I was able to find the relevant info in the manual which I
> overlooked/did not understand before.
> The 'mystery' of the energy drop at restart appears
> to be solved, even though I haven't tried the restart using the rstdip
> file yet. As for the energy drift during NVE run, however, I did few
> more tests and I am now even more puzzled than before:
>
> (1) The original 1 ns NVE run, 1 fs timestep, ipol=1, default for
> polarizable potential:
> Etot=-6592.0065 for NSTEP=1, then within few ps Etot goes up to
> -6575.1718 and then steadily decreases to -6588.2209 at the end of 1ns
> run - drop of some 13 kcal/mol from the highest value, however, still
> above the initial value for NSTEP=1.
>
> (2) I tried indmeth=1 (in the &ewald section of the input), everything
> else the same:
> Etot=-6592.0065 for NSTEP=1 (same as above), but then Etot steadily
> decreases and drops by more than 200 kcal/mol to -6881.6926 in just
> 200 ps !!
>
> (3) Then I tried a NVE run with polarizability OFF (ipol=0), starting
> from the same initial configuration as (1) and (2). The initial Etot is
> of course different and there is a short (10-20 ps) 'equilibration'
> period when the energy jumps a bit (within 3 kcal/mol) as the initial
> configuration was obtained with polarizable potential, but apart from
> that Etot remains oscilating around a pretty much constant value with a
> drift of 0.5 kcal/mol at most over 700 ps.
>
> Now, it is very well possible that I overlooked something painfully
> obvious and out of ignorance am doing something terribly wrong.
> But I am really worried because I have been routinely using AMBER with
> polarizable potential for my simulations of slab systems in last few
> years. So far I always did constant temperature simulations, and never
> noticed anything alarming. However, the strange behavior of constant
> energy simulation combined with polarizable potential brings up a
> question of how reliable all my previous simulation are. Can it not be
> that the velocity scaling due to the temperature control just masks the
> problem with polarizable force field for slab systems?
>
> I would be grateful for additional help/comments/suggestions.
> best regards
>
> Martina Roeselova
>
>
>
>
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