Re: [AMBER] Sorry again..this is right

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 1 Jun 2011 10:02:11 -0400

Hi,

Just to back up Dave's point, here are results showing energy for
ascii write vs netcdf write in PMEMD on 1 CPU - the difference is
zero. Another way to show that what you are seeing is unrelated to
choice of output trajectory format would be to perform a 3rd ascii run
and compare it to your previous ascii run; you should start to see
similar variations after a while.

-Dan

On Wed, Jun 1, 2011 at 7:49 AM, David A Case <case.biomaps.rutgers.edu> wrote:
> On Wed, Jun 01, 2011, Lorenzo Gontrani wrote:
>> ASCII
>>
>>  NSTEP =   800000   TIME(PS) =  123410.000  TEMP(K) =   500.05  PRESS =
>> 0.0
>>  Etot   =      8096.9458  EKtot   =      5121.5291  EPtot      =
>> 2975.4167
>>  BOND   =      1914.0149  ANGLE   =      2358.0329  DIHED      =
>> 681.4969
>>  1-4 NB =       167.8290  1-4 EEL =       706.2125  VDWAALS    =
>> -2310.5917
>>  EELEC  =      -541.5777  EHBOND  =         0.0000  RESTRAINT  =
>> 0.0000
>>  Ewald error estimate:   0.1526E-02
>>
>> BINARY
>>
>>
>>  NSTEP =   800000   TIME(PS) =  123410.000  TEMP(K) =   500.07  PRESS =
>> 0.0
>>  Etot   =      8094.2782  EKtot   =      5121.6841  EPtot      =
>> 2972.5941
>>  BOND   =      1914.4745  ANGLE   =      2356.1170  DIHED      =
>> 682.1608
>>  1-4 NB =       167.6396  1-4 EEL =       707.7357  VDWAALS    =
>> -2310.7221
>>  EELEC  =      -544.8114  EHBOND  =         0.0000  RESTRAINT  =
>> 0.0000
>>  Ewald error estimate:   0.1476E-02
>>
>
> Please see section 1.3.4 of the Amber11 manual about roundoff errors in MD.
> Since pmemd does dynamic load balancing, the division of tasks among
> processors may change from one run to the next.  This affects the order of
> arithmetic manipulations, and hence to differences among trajectories that
> otherwise would be the same.
>
> You can run a test with a single thread, and should see the discrepancies go
> away.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


E.jpg
(image/jpeg attachment: E.jpg)

Received on Wed Jun 01 2011 - 07:30:03 PDT
Custom Search