Hi, Rachel,
Since there is no bond angle constrain in SANDER or other programs, to make
the molecule linear, you need to set three bonds (just as in the case in
water where an extra H-H bond was placed for contraining to rigid triangle).
Of course, you need to make sure that HH bond is exactly twice as long as
the DH-H bonds.
Secondly, you may want to put a mass on DH. This inevitably changes the mass
distribution of the system. So, if you are interested in how the molecule
rotates (how fast or slow), you probably should be careful. But you still
can do this because the difference is only a simple correction term. If you
are ok with a molecular that otherwise rotates a bit faster or if you are
interested in only the thermodynamic or equilibrium property, this could be
the choice.
Another option is that you manually modify the code to treat DH as an "extra
point" to place whatever the force acting on it to the real H's and update
it's movement simply by geometry consideration not by force/velocity.
Hope this helps and good luck!
yong
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Rachel
Sent: Monday, November 13, 2006 9:09 AM
To: amber.scripps.edu
Subject: Re: AMBER: vlimit exceeded for step 0, vmax = infinity
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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Nov 15 2006 - 06:07:24 PST
