we already answered this question. Both trajectories
are valid, they are just different. Your system could
do either of these. You now have two trajectories.
Behavior that is the same between them is probably
more reliable than things that are not the same.
Carlos
----- Original Message -----
From: "sychen" <yuann.bioinfo.ndhu.edu.tw>
To: <amber.scripps.edu>
Sent: Saturday, March 06, 2004 8:40 PM
Subject: Re: AMBER: Sander problem with different CPU
> Thanks for you & Carlos Simmerling
>
> I've compared my MD simulation with different cpu, and the difference
> gets larger during the production dynamics. I make a comparison between
> them about the RMSd, as follows,
> http://bioinfo.ndhu.edu.tw/~yuann/TMP/1.gif
>
> I'd like to know how to explain my result reasonably, or I have to run
> the simulation with only one CPU ?
> Thank you very much!
>
>
> Sincerely,
> sychen.
>
>
> On Fri, 5 Mar 2004 08:39:37 -0500
> "Robert Duke" <rduke.email.unc.edu> wrote:
>
> > Yuann -
> > You should not be surprised. When sander runs on different numbers of
> > cpu's, the calculations are done in a different order, because the
> > calculations are distributed differently. This causes differences in
the
> > rounding errors, and ultimately the results will drift around a bit.
The
> > results you are seeing here are perfectly acceptable, and if you look at
the
> > pairlist totals, the same sorts of pairlists are being generated, the
only
> > difference is they are distributed in the 8 processor case.
> > I typically see identical output for no more than around 300 steps in
MD,
> > and for some systems, a value or two will vary in far fewer steps in the
> > last digit, due to the fact that the value as printed out is very near
the
> > "rounding point", and can easily go one way or the other (thus a value
> > reported as 1.4378 vs 1.4377 may actually be reflecting an internal
> > difference of 1.437750000000001 vs. 1.437749999999999).
> > Regards - Bob Duke
> > ----- Original Message -----
> > From: "yuann" <yuann.bioinfo.ndhu.edu.tw>
> > To: <amber.scripps.edu>
> > Sent: Friday, March 05, 2004 7:29 AM
> > Subject: AMBER: Sander problem with different CPU
> >
> >
> > > Dear All,
> > > Recently, I'm supprised that sander gives me different output
> > > when it applies different number of CPU on IBM P690(AIX51). The
> > > difference between them initiates at 550steps, and gets larger
> > > at the NPT equlibrium stage, and also production dynamics.
> > > System administrator for this machine told me all the AMBER bugfix
> > > are updated to fix.36.
> > >
> > > I'm wondering if this is due to the arrangement of 'SIZE OF NONBOND
LIST'
> > > while running sander with different number of CPU?
> > >
> > >
> > > Here are the output information at the 1st minimization step,
> > >
> > >
> > >
> > > ---input for sander minimization---
> > > DNA_drug_complex_WAT 11578atoms 1st_Minimization 1000steps
> > >
> > > &cntrl
> > > imin=1, ntx=1, maxcyc=1000, ncyc=200,
> > > ntc=1, ntf=1,
> > > ntb=1, ntp=0,
> > > ntpr=50,
> > > cut=9.0,
> > > ntr=0,
> > > &end
> > > &ewald
> > > &end
> > >
> > > --------main difference of output-------
> > >
> > > (1cpu):
> > > | Local SIZE OF NONBOND LIST = 2461494
> > > | TOTAL SIZE OF NONBOND LIST = 2461494
> > >
> > > (8cpu):
> > > | Local SIZE OF NONBOND LIST = 370628
> > > | TOTAL SIZE OF NONBOND LIST = 2461494
> > >
> > > ----------------------------------------
> > >
> > > (1cpu):
> > > NSTEP ENERGY RMS GMAX NAME
NUMBER
> > > 550 -4.6614E+04 9.7806E-01 2.2339E+01 O5'
543
> > >
> > > BOND = 3037.9037 ANGLE = 176.5293 DIHED =
555.3168
> > > VDWAALS = 7046.6932 EEL = -56278.6230 HBOND =
0.0000
> > > 1-4 VDW = 341.6471 1-4 EEL = -1493.6799 RESTRAINT =
0.0000
> > >
> > > ..........
> > >
> > > (8cpu):
> > > NSTEP ENERGY RMS GMAX NAME
NUMBER
> > > 550 -4.6614E+04 9.7805E-01 2.2339E+01 O5'
543
> > > BOND = 3037.9031 ANGLE = 176.5292 DIHED =
555.3168
> > > VDWAALS = 7046.6917 EEL = -56278.6196 HBOND =
0.0000
> > > 1-4 VDW = 341.6471 1-4 EEL = 1493.6799 RESTRAINT =
0.0000
> > >
> > > ..........
> >
> --------------------------------------------------------------------------
> > -
> > >
> > >
> > > sincerely,
> > > sychen.
> > >
> >
> -----------------------------------------------------------------------
> > > 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 Mon Mar 08 2004 - 14:53:01 PST
