AMBER Archive (2006)

Subject: Re: AMBER: how to include EXTRA POINTS in AMBER8

From: Rachel (comeonsos_at_googlemail.com)
Date: Mon Dec 04 2006 - 11:03:11 CST

Dear David,

Thanks for your reply. I have tried to put a finite mass on that extra point
(I used mass = 1.008 as the normal hydrogen atom), and the result is even I
used very very small timestep (e.g. 0.1fs), I don't have any problem with
vlimit, and the error message is:
####################################################################
 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
 Etot = -217128.3786 EKtot = 0.0000 EPtot = -
217128.3786
 BOND = 400.3220 ANGLE = 2165.2216 DIHED =
6798.3874
 1-4 NB = 2513.3831 1-4 EEL = 34285.2873 VDWAALS =
25111.1035
 EELEC = -288402.0835 EHBOND = 0.0000 RESTRAINT =
0.0000
 Ewald error estimate: 0.8763E-04
 ------------------------------------------------------------------------------

     Coordinate resetting (SHAKE) was not accomplished
     within 3000 iterations

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.
#####################################################################

And about the name, I used 'EPH' and in xleap, I defined its type as 'EP',
and element 'Lp', which is the same as TIP4P, TIP5P water.

Thanks a lot for your kind concern, and I really appreciate your help and
suggestions.

Best regards,
Rachel

On 12/4/06, David A. Case <case_at_scripps.edu> wrote:
>
> On Mon, Dec 04, 2006, Rachel wrote:
> >
> > I have been trying to include some massless extra points in my system,
> > however not successful, and the program kept complaining that 'vlimit
> > exceeded for step 0, vmax=infinity',
>
> First, did you try making the masses non-zero to see if the error changes
> or
> goes away?
>
> Second, do the names of your extra point atoms begin with the letters
> "EP"?
>
> ...dac
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