Dear Carlos,
Yes, I obtained the same energies in both queues setting ntpr=1,
So it is a problem of roundoff errors of integration steps ?
Thanks
Cristian Obiol
Biological Systems Modelling and Drug Design
Research Group
University of Barcelona
> it might be easier to run 500 steps of MD and set ntpr to 1.
> do they match? as Dave Case said in his reply, if the initial
> forces are not too high, this should work.
>
> cristian obiol wrote:
> > Dear Carlos,
> > The ntpr is set to 1000, my problem was that i killed the two jobs (4p
> > 8p) in the first steps because i noticed that the error between the
> > energies grew up,
> > Now I carried out the jobs to the final and the errors only oscilates
> > between 5 to 107 of 157,000 Kcal/mol and in an aleatory way.
> > This variations in the total energy in 4/8 processors can be normal,
> > I'm right ??
> >
> >
> > Thanks in advance.
> >
> > Cristian Obiol
> > Biological Systems Modelling and Drug Design
> > Research Group
> > University of Barcelona
> >
> >> in the third MD step (of ~1fs each) or third time that the
> >> energy is written in the output (which could be longer)?
> >> I get identical output for different # of cpus up to a few hundred
> >> steps of 1fs each.
> >>
> >> cristian obiol wrote:
> >>> Dear AMBER users,
> >>>
> >>> We have running a cluster of 12 processors in linux Debian platform
> >>> (mpich 1.2.6. and fortran intel_fc_80 compiler), and our results in
> >>> sander8 outputs are different depending the queue (4 or 8) that we are
> >>> using, around 0.0001 % in the final energy in the third step.
> >>>
> >>> We are disturbed because the test factor_ix for sander 8 is well passed
> >>> in both queues.
> >>>
> >>> Any comments are welcome,
> >>> Thanks in advance.
> >>>
> >>> Cristian Obiol
> >>> Biological Systems Modelling and Drug Design
> >>> Research Group
> >>> University of Barcelona
> >>> -----------------------------------------------------------------------
> >>> 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
> >
> > -----------------------------------------------------------------------
> > 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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Feb 26 2006 - 06:10:07 PST
