AMBER Archive (2006)

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

From: Rachel (comeonsos_at_googlemail.com)
Date: Mon Dec 04 2006 - 12:35:08 CST

Dear David,

Thanks for your previous reply. As I said in my last email, when I put some
finite mass on the extra point atom, the error message did change, so I was
thinking the extra points in my system may not have been read correctly.
What I want to make sure at the moment is that do I actually need to modify
the AMBER source code (like extra_pts.f) in order to make sander recognize
extra points? or it is because some mistakes in the way I treated extra
points resulted in this error? And do you have any suggestions if I need to
modify the code or any idea where might be error came from?

Thank you so much!
Best regards,
Rachel

On 12/4/06, Rachel <comeonsos_at_googlemail.com> wrote:
>
> 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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>
>

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