Hiya, amber users,
I have added some mass to the DH atom as Yong suggested, however, i still
have error messages when i started to run md, as follows:
--------------------------------------------------------------
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 5 65721215812159
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
------------------------------------------------------------------------
I dont quite understand what does it mean? and also the bond energy of 1st
step md is still differeent from the last step of the minimization.
Does anyone has any idea about this please?
Thanks very much.
Rachel
On 11/14/06, Yong Duan <duan.ucdavis.edu> wrote:
>
>
> 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
>
-----------------------------------------------------------------------
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 - 06:07:36 PST
