Hi all,
In my quest to find a legacy version of Amber, I managed to get sander from
Amber5 working but have a couple of questions on translating some of the
old sander inputs into the modern version, ie in the ala dipeptide example,
there's an example input as-
#minimization
> &cntrl
> IREST = 0, IMIN = 1, NTX = 1,
> MAXCYC = 100, NCYC = 100, NTMIN = 1,
> NTB = 1,
> DX0 = 0.0002, DXM = 1.0, DELE = 0.0001, DRMS = 0.001,
> NRUN = 0, NSNB = 500, CUT = 6.25, SCEE = 2.0, IDIEL = 1,
> NTPR = 50,
> &end
>
Most of the variables seem to have carried over in some way, but I'm a
little confused on how the dielectric portion is handled.
The Amber5 manual mentions two dielectric functions (idiel=0 for distance,
idiel=1 for constant) with the dielc controlling the constant. So if I
wanted a minimization with a constant dielectric of 4 in gas, I think I'd
have it in the old style as
#min old sander
> &cntrl
> IREST = 0, IMIN = 1, NTX = 1,
> MAXCYC = 50, NCYC = 10, NTMIN = 1,
> NTB = 0,
> DX0 = 0.0002, DXM = 1.0, DELE = 0.0001, DRMS = 0.001,
> NRUN = 0, NSNB = 500, CUT = 12, SCEE = 1.2, IDIEL = 1,
> NTPR = 50, dielc=4,
> &end
>
But I'm not clear on is how this would translate to amber16 sander? I think
if I want a gas phase with a dielectric of 4 I'd use
#current min
> &cntrl
> ...
> igb=0, extdiel=4,
> ...
> &end
> /
>
But I'm a little confused if this is actually doing the same thing- I know
there's the dielc variable also, but my reading of it is the dielc is only
used for distance dependent dielectric functions instead of a constant
dielectric value? Therefore
igb=0, dielc=4,
> ...
> &ewald
> eedmeth=5,
> &end
>
Should be the same as the following?
NRUN = 0, NSNB = 500, CUT = 12, SCEE = 1.2, IDIEL = 1,
> NTPR = 50, dielc=4,
>
Lastly, what exactly is the DELE variable? It shows up a couple of times in
the Amber5 manual in example inputs, but I can't find any documentation of
what it actually is.
Best,
Kenneth
--
Ask yourselves, all of you, what power would hell have if those imprisoned
here could not dream of heaven?
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Received on Mon Dec 21 2020 - 08:30:02 PST
