On Fri, Mar 14, 2008, Paul Johns wrote:
> I'm fairly new to AMBER, and I've been having some troubles. I have
> been trying to run MD on a 40 angstrom box of POL3 water molecules, but
> it doesn't seem to be working. In particular, my error comes in when I
> try to heat the box of water from 0 K to 300 K. I built the box in Leap
> using the leaprc.ff02 force field and the following commands:
>
> WAT = PL3
> loadAmberParams frcmod.pol3
> solvatebox PL3 POL3BOX 20.0
> saveamberparmpol PL3 pol3_2.prmtop pol3_2.inpcrd
>
> This structure seems to be fine, so my next step is minimization. I
> minimized rather simply, using the following as the input file:
>
> &cntrl
> ipol = 1,
> imin = 1,
> maxcyc = 25000,
> ncyc = 10000,
> ntb = 1,
> ntr = 0,
> cut = 8,
> /
>
> A bit excessive on the minimization steps, I know. This seems to be OK,
> as well. Now here's my trouble step, heating. I used the following for
> the input:
>
> &cntrl
> ipol = 1,
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 1,
> cut = 8,
> ntr = 0,
> ntc = 2,
> ntf = 2,
> tempi = 0.0,
> temp0 = 300.0,
> ntt = 1,
> nstlim = 10000, dt = 0.0002,
> ntpr = 100, ntwx = 100, ntwr = 1000,
> /
I think you have to set indmeth=1 (not the default of 3) until you have an
equilibrated sample. If you look at the dipole temperatures you get, you
will probably see crazy behavior there. In spite of what Thomas suggested,
don't turn off SHAKE.
This should be in the manual.
You say that you are "fairly new to Amber": be sure that you have a good
reason for running polarizable potentials. None of them are as well tested as
the fixed-charge force fields, and the detailed way in which polarizability
should be represented is still a matter of active research.
...dac
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Received on Sun Mar 16 2008 - 06:07:49 PDT
