Dear Dr Walker:
I try to print dipole moment in the classical simulation, I still has
problems. My input file is in following part:
&cntrl
imin = 0, ntb = 0,
igb = 0, ntpr = 1, ntwx = 1,
ntt = 3, gamma_ln = 3.0,
tempi = 40.0, temp0 = 40.0,
nstlim = 10000, dt = 0.001,
cut = 10.0,
&end
&dipoles
group1
RES 1
END
END
&end
In my simulation, just one residue was involved. So, I want to calculate the
dipole moment of this residue.
The error information is in the following part: I think my input should have
some problems, but I do not know where it is. Would you like to give me some
suggestions. Thanks in advance. In addition, I used Amber 10.
NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 42.12 PRESS =
0.0
Etot = 42.0427 EKtot = 3.0131 EPtot =
39.0296
BOND = 0.6243 ANGLE = 2.1260 DIHED =
13.6633
1-4 NB = 4.4137 1-4 EEL = 134.9488 VDWAALS =
-1.7414
EELEC = -115.0051 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
------------------------------- DIPOLE INFO
----------------------------------
NSTEP = 1 TIME(PS) = 0.001
rfree: End of file on unit 5
On Mon, Aug 23, 2010 at 12:16 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> > The following is my input file:
> > vacu
> > &cntrl
> > imin = 0, ntb = 0,
> > igb = 0, ntpr = 200, ntwx = 200,
> > ntt = 3, gamma_ln = 3.0,
> > tempi = 0.0, temp0 = 0.0,
> > nstlim = 1000000, dt = 0.001,
> > cut = 12.0,ifqnt=1,
> > /
> > &qmmm
> > qmmask=':1-2'
> > qmshake=0,
> > qmcharge=0,
> > qm_theory='PM3',
> > qmcut=12.0,
> > /
> > &dipoles
> > end
> > &end
>
> Of course this doesn't work, you haven't specified any of the dipoles to
> actually print. This was my very first point. Does it work classically?
> Clearly you didn't test this.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
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--
Best Wishes
Sincerely Yours
Hong-bin Xie
---------------------------------------------------------------
Hong-bin Xie
Postdoctoral Researcher
Department of Chemistry
University of California at Irvine
Email:xhbxhb1980224.gmail.com <Email%3Axhbxhb1980224.gmail.com>
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Received on Tue Sep 07 2010 - 10:30:03 PDT
