I have also set up an anion/water system with amoeba and when I try to print
the induced dipole on the anion, I get strange results. Here is my
sander input:
/////////////////\\\\\\\\\\\\\\\\\\\\
500 ps MD Run
&cntrl
nstlim = 400000, dt = 0.00125, t = 0.0,
ntpr = 400, ntwe = 400, ntwx = 400,
ntx = 5, irest = 1,
jfastw = 4,
cut = 11.0, ibelly = 1, bellymask = "!.1",
ntt = 2, tempi = 298.15, temp0 = 298.15, vrand=200, ig=-1,
iamoeba=1, ntb = 1, iwrap = 1, nscm = 1,
/
&ewald
order=6,
/
&amoeba
dipole_scf_tol=1e-4, do_vdw_taper=1, do_vdw_longrange=1,
/
&dipoles
Chloride
ATOM 1
END
END
/
GROUPS
END
END
\\\\\\\\\\\\\\\\\\\\/////////////////
Which seemed to require the extra GROUPS section at the end to prevent
EOF errors due to the way the &dipoles section is re-read on each
output. Anyway, the resulting dipoles printed as expected on a
similar system using SPC/E water and ipol=1 polarizability for the
anion, but are giving obviously incorrect numbers for the amoeba run.
$ grep "DIPGRP - 1: total dipole :" run.log
DIPGRP - 1: total dipole : -4.803 -4.006 2.003 6.567 D
DIPGRP - 1: total dipole : -4.803 -4.006 2.003 6.567 D
DIPGRP - 1: total dipole : -4.803 -4.006 2.003 6.567 D
DIPGRP - 1: total dipole : -4.803 -4.006 2.003 6.567 D
DIPGRP - 1: total dipole : -4.803 -4.006 2.003 6.567 D
DIPGRP - 1: total dipole : -4.803 -4.006 2.003 6.567 D
DIPGRP - 1: total dipole : -4.803 -4.006 2.003 6.567 D
DIPGRP - 1: total dipole : -4.803 -4.006 2.003 6.567 D
Should I expect the &dipoles section to work for amoeba or is there a
separate facility for printing dipoles?
Also, is there a convenient way to re-run through an already-made
mdcrd trajectory and calculate this so I don't waste computer time?
Thanks in advance,
~ David Rogers
Dr. Thomas Beck Lab
Department of Chemistry
University of Cincinnati
On Tue, Oct 14, 2008 at 1:25 PM, Zhao, Zhen (zhaozh)
<zhaozh.ucmail.uc.edu> wrote:
> Hi, all
>
> I have run a simulation with the AMOEBA force field with a chloride ion in bulk water. I print out the induced dipole by specifying
> a dipole section at the end of the input file as the following:
>
> &dipoles
> Chloride
> ATOM 646
> END
> END
> /
> GROUPS
> END
> END
>
> The induced dipole of the chloride ion is around 5 debyes in the output file, which is far beyond the expected value(should not exceed 1 Debye, I think). I donot know if anything wrong in the code or the way I set up. Thanks in advance for your help!
>
> Sincerely
>
> Zhen
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Received on Wed Oct 15 2008 - 05:11:16 PDT
