Hi, all,
Thanks very much for all your replies, they helped me a lot. In regarding to
the vmax= infinity, i think Yong was right, there is a massless atom in my
system. It is a dummy atom in the hydrogen molecule model i built up. I
built up the model according to another paper. and this is how it describes
the model:
The hydrogen molecule model of Hunter et al. -- this is a three point
molecule with two atoms and a dummy placed at their midpoint, only the two
atoms have mass and only the dummy has non-zero lennard-Jones parameters.
All atoms/dummy have partial charges, necessary to simulate the
experimentally observed quadrupole, the charges for the two hydrogen atoms
are 0.475 and -0.95 for the dummy, adding to a total charge of zero, the
bond distance used is 0.7A.
And the way i built up the model was 1st wrote a pdb file like this:
-----------------------------------------------------------------------------------------------
ATOM 1 HD HH2 1 -2.906 1.541 0.000 1.00 0.00
ATOM 2 DH HH2 1 -3.648 1.541 0.000 1.00 0.00
ATOM 3 HD HH2 1 -4.390 1.541 0.000 1.00 0.00
TER
END
----------------------------------------------------------------------------------------------
And then load it in xleap and edit the charges, atom type etc. and save as
.lib file, and i also wrote the .frcmod file like this:
----------------------------------------------------------------------------------------------
# H2 molecule parameters
MASS
HD 1.008
DH 0.000
BOND
HD-DH 150.00 0.960
ANGLE
HD-DH-HD 500.0 180.0
DIHEDRAL
IMPROPER
NONBON
HD 0.000 0.000
DH 2.920 0.272
------------------------------------------------------------------------------------------
In which the dummy atom DH is massless.
What I want to ask now is, 1) is this the right way to build a molecule and
is there any mistake in the parameters i used according to the model? 2) As
according to the model description, the dummy should be massless, so how
can i use the 'correct model' while solve the infinity velocity problem? 3)
are there any other hydrogen molecule models i can use instead of this one?
for example a model without this dummy, just two normal hydrogen atoms?
Thanks very much for your kind help.
Best regards,
Rachel
On 11/10/06, Yong Duan <duan.ucdavis.edu> wrote:
>
>
> Hi, Rachel,
>
> I wonder what would happen if you set ntc=3 in minimization and MD. I know
> it will not converge and I understand this is not recommended by the
> manual,
> but just perform a 100-step minimization after you do those "standard"
> minimization.
>
> Another wild guess, could it be possible that one of the atoms in your
> system has zero mass? If it is a very high velocity, it will say a number
> of
> a lovely "****". But, if the print out is "Infinity", it means "divided by
> a
> zero" somewhere. This could either be two atoms happen to be right on top
> of
> each other or some atoms are simply massless.
>
> Another suggestion is to try simulations on the individual components to
> identify which part of the system may cause the trouble.
>
> Good luck!
>
> yong
> -----Original Message-----
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of
> Rachel
> Sent: Friday, November 10, 2006 7:54 AM
> To: amber.scripps.edu
> Subject: Re: AMBER: vlimit exceeded for step 0, vmax = infinity
>
>
> Hi, all,
>
> I followed the tutorial 1 and the tutorial of non-standard residue, and i
> did try to simulate only the hydrogen molecule with explicit water and it
> was fine as well :(
>
> Any other suggestions, now i really dont know where shall i start to solve
> the problem ::>_<:: any suggestion will be greatly appreciated.
>
> best regards,
> Rachel
>
>
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Received on Wed Nov 15 2006 - 06:07:18 PST
