Dear Dmitry
Is this about the 'time' being printed 'wrong' ? Sees to be so. However,
how could this possibly matter ? The time printed there can be easily
computed from NSTEP*dt, and in fact is referenced to the first step
time. You could easily change that by changing the initial restart file
times stamp at the top.
Second, and perhaps more important, you seem to be writing your mdout
file every 500 steps ! Is this really needed ? Unless yous system is
really small, you are probably wasting time doing that and you mdout
would be HUGE. I would change ntpr to 10000 or even more.
If you are also writing the mdcrd file this often, I am afraid for your
disk ! ;-)
Adrian
On 1/3/12 10:49 AM, Dmitry Mukha wrote:
> Here is something unexpected with time counter. I guess there is a rounding
> error. System information is provided below.
>
> Calculated by pmemd.cuda on GTX 580 with stable temperature 74 C upon
> running.
>
> NSTEP =167945000 TIME(PS) = 335990*.000* TEMP(K) = 301.78 PRESS
> = 0.0
> Etot = -43870.1125 EKtot = 10373.3535 EPtot =
> -54243.4660
> BOND = 115.6680 ANGLE = 323.6944 DIHED =
> 390.0954
> 1-4 NB = 115.1031 1-4 EEL = 941.7038 VDWAALS =
> 7478.2460
> EELEC = -63607.9767 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> ------------------------------------------------------------------------------
>
> wrapping first mol.: 202.98562552576283 -143.53251062694440
> 49.721126343645942
>
> NSTEP =167945500 TIME(PS) = 335990*.999* TEMP(K) = 298.40 PRESS
> = 0.0
> Etot = -43868.9224 EKtot = 10257.1758 EPtot =
> -54126.0981
> BOND = 106.1077 ANGLE = 315.2293 DIHED =
> 395.9334
> 1-4 NB = 132.9285 1-4 EEL = 939.2730 VDWAALS =
> 7504.5162
> EELEC = -63520.0861 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> ------------------------------------------------------------------------------
>
> check COM velocity, temp: 0.000039 0.00(Removed)
> wrapping first mol.: 202.98562552576283 -143.53251062694440
> 49.721126343645942
>
> NSTEP =167946000 TIME(PS) = 335991*.999* TEMP(K) = 296.82 PRESS
> = 0.0
> Etot = -43865.2240 EKtot = 10203.1387 EPtot =
> -54068.3627
> BOND = 107.7294 ANGLE = 329.0983 DIHED =
> 377.3811
> 1-4 NB = 122.6458 1-4 EEL = 950.4681 VDWAALS =
> 7709.3740
> EELEC = -63665.0594 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> ------------------------------------------------------------------------------
>
> wrapping first mol.: 202.98562552576283 -143.53251062694440
> 49.721126343645942
>
> NSTEP =167946500 TIME(PS) = 335992*.999* TEMP(K) = 300.10 PRESS
> = 0.0
> Etot = -43866.7111 EKtot = 10315.6191 EPtot =
> -54182.3302
> BOND = 121.0231 ANGLE = 317.1874 DIHED =
> 399.7288
> 1-4 NB = 130.4573 1-4 EEL = 940.9642 VDWAALS =
> 7383.4841
> EELEC = -63475.1751 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> ------------------------------------------------------------------------------
>
>
> *uname -a*
> 2.6.35.14-106.fc14.x86_64 #1 SMP Wed Nov 23 13:07:52 UTC 2011 x86_64 x86_64
> x86_64 GNU/Linux
>
> *gcc -v*
> Using built-in specs.
> COLLECT_GCC=/usr/bin/gcc
> COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.5.1/lto-wrapper
> Target: x86_64-redhat-linux
> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
> --infodir=/usr/share/info
> --with-bugurl=http://bugzilla.redhat.com/bugzilla--enable-bootstrap
> --enable-shared --enable-threads=posix
> --enable-checking=release --with-system-zlib --enable-__cxa_atexit
> --disable-libunwind-exceptions --enable-gnu-unique-object
> --enable-linker-build-id
> --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,lto --enable-plugin
> --enable-java-awt=gtk --disable-dssi
> --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre
> --enable-libgcj-multifile --enable-java-maintainer-mode
> --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib
> --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686
> --build=x86_64-redhat-linux
> Thread model: posix
> gcc version 4.5.1 20100924 (Red Hat 4.5.1-4) (GCC)
>
> *./nvcc --version*
> nvcc: NVIDIA (R) Cuda compiler driver
> Copyright (c) 2005-2010 NVIDIA Corporation
> Built on Wed_Nov__3_16:16:57_PDT_2010
> Cuda compilation tools, release 3.2, V0.2.1221
>
--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Tue Jan 03 2012 - 08:00:05 PST
