2013 Nobel Prize for Chemistry awarded to Warshel, Levitt and Karplus

This year, the Nobel Prize for Chemistry has a special flavor for computational biochemists, as the Swedish Academy has decided to recognize the creators of Quantum Mechanics/Molecular Mechanics hybrid methods. Levitt and Warshel developed the first computational simulation of a protein, back in 1975, whereas Karplus and his group developed the well-known CHARMm force-field and molecular dynamics code. I am very glad  to see Warshel recognized as the towering giant he really is (in spite of his short stature).  He is a very warm and likeable fellow, always eager for a good discussion on the merits (and demerits) of a scientific proposal. He does have, however, a singular lack of patience for bullshit, and a peculiar disregard for diplomatic niceties ....

Warshel's parents were Polish Jews who left Europe for Palestine before World War II to join a kibbutz. He attributes part of  his peculiar temper to the circumstances of growing up in such an utopian socialist community in the 1940's, before the Israeli War of Independence. Lying and "truth embellishment" were very strongly frowned upon, and one was expected to be able to withstand withering criticism whenever warranted. His BS-detector is therefore quite over-calibrated, and he takes no prisoners when arguing against a wrong-headed argument. Warshel's abrasive style is well-known in the computational chemistry, as are is frequent controversies with other workers.

He also told me one of the best jokes I know... He presented it as a real tale of his uncle's exploits as an officer in the Polish Army. here it goes:

During on of his official leaves, his uncle went to a brothel. After the "job" had been done, he got up to get dressed and leave. The prostitute the asked: "What about the money, sir?". And he replied: "An officer never accepts money, my lady"

Gamess (US) frequently asked questions Part 5: "THE VIBRATIONAL ANALYSIS IS NOT VALID"

Gamess (US) and Firefly by default assume geometric convergence has been achieved when the maximum gradient is below 1e-4 and the RMS gradient is smaller  than 1/3 of the maximum gradient.  This convergence criterion may be changed by the user with


 $STATPT OPTTOL=<your desired convergence criterion> $END


It is well known that the vibrational analysis is strictly valid mathematically when the Hessian is computed in true stationary points (i.e when the gradient is exactly equal to zero). If the maximum gradient is sufficiently close to zero, the vibrational analysis (although not absolutely correct) is still close enough to the "true" solution for all practical purposes.



This introduction brings us to today's FAQ. A recurring question in both the Gamess-US list and the Firefly forums concerns the message often printed by the program after a vibrational analysis:

*THIS IS NOT A STATIONARY POINT ON THE MOLECULAR PES THE VIBRATIONAL ANALYSIS IS NOT VALID*

This message arises from the way gradients are analyzed by Gamess: gradients are originally computed in one set of coordinates (cartesian coordinates, I believe) , and then transformed into the  coordinate system specified by the user. Optimizations stop when the "transformed gradient" lies below OPTTOL, but Gamess uses the original, non-transformed, gradient to decide whether to consider the geometry as a stationary point on the molecular PES.  Therefore, if  the geometry is converged, the scary message in capital letters above may be safely disregarded. When in doubt, simply decrease your OPTTOL value, continue the optimization and re-compute the hessian.

Gamess (US) frequently asked questions Part 4: The rungms script

Third guest post by Kirill Berezovsky (Petrozadovsk State University).

Gamess (US) is run though a script provided in the installation package. This script MUST be adapted by the user. The rungms-script below has been adapted to be used with the Gamess (US) installation described in earlier posts. Happy computing :-)

RUNGMS script

#!/bin/csh

set SCR=/scr/$USER

set USERSCR=~$USER/scr

set GMSPATH=/usr/local/gamess

set JOB=$1

set VERNO=$2

if ($VERNO == cpu) set TARGET=mpi

if ($VERNO == gpu) set TARGET=ga

if (null$VERNO == null) set VERNO=cpu

set master=`hostname`

printf "\n * Started at:           `date`"

set DSK=`df -m $SCR | awk 'NR==2{print$4}'`

printf "\n * Available disk space: $DSK MB"

printf "\n * Temporary files in:   $SCR and in $USERSCR\n\n"

limit stacksize 8192

if ($JOB:r.inp == $JOB) set JOB=$JOB:r

if (-e $JOB.inp) then

   cp  $JOB.inp  $SCR/$JOB.F05

else

   echo "Input file $JOB.inp not found"

   exit 4

endif

source $GMSPATH/gms-files.csh

if (-e $HOME/.gmsrc) source $HOME/.gmsrc

set ngddi=`grep -i '^ \$GDDI' $SCR/$JOB.F05 | grep -iv 'NGROUP=0 ' | wc -l`

if ($ngddi > 0) then

   set GDDIjob=true

   echo "This is a GDDI run, keeping various output files on local disks"

   set echo

   setenv  OUTPUT $SCR/$JOB.F06

   setenv   PUNCH $SCR/$JOB.F07

   unset echo

else

   set GDDIjob=false

endif

if ((-e $PUNCH) || (-e $MAKEFP) || (-e $TRAJECT) || (-e $RESTART) ) then

   echo "Please save, rename, or erase these files from a previous run:"

   echo "     $PUNCH,"

   echo "     $TRAJECT,"

   echo "     $RESTART, and/or"

   echo "     $MAKEFP,"

   echo "and then resubmit this computation."

   exit 4

endif

#----------------------------------------------------------------------

if ($TARGET == mpi) then

 set NCPUS=`grep cores /proc/cpuinfo | wc -l`

 echo " * CPU cores:   $NCPUS "

 echo " * GPU devices: not used"

 echo " "

 setenv TRAJECT $USERSCR/$JOB.trj

 setenv RESTART $USERSCR/$JOB.rst

 setenv INPUT $SCR/$JOB.F05

 setenv PUNCH $USERSCR/$JOB.dat

 if ( -e $TRAJECT ) rm $TRAJECT

 if ( -e  $PUNCH ) rm $PUNCH

 if ( -e  $RESTART ) rm $RESTART

 setenv LD_LIBRARY_PATH /opt/intel/impi/4.0.2.003/intel64/lib:$LD_LIBRARY_PATH

 set path= ( /opt/intel/impi/4.0.2.003/intel64/bin $path )

mpdboot

 mpiexec -n $NCPUS $GMSPATH/gamess.$VERNO.x

mpdallexit

 cp $PUNCH .

endif

#----------------------------------------------------------------------

if ($TARGET == ga) then

 set PPN=1

 set NCPUS=1

 @ NPROCS = $NCPUS

 setenv HOSTFILE $SCR/$JOB.nodes.mpd

 if (-e $HOSTFILE) rm $HOSTFILE

 touch $HOSTFILE

  

 echo `hostname` >> $HOSTFILE

 set NNODES=1

 setenv PROCFILE $SCR/$JOB.processes.mpd

 if (-e $PROCFILE) rm $PROCFILE

 touch $PROCFILE

 echo "-n $NPROCS -host `hostname` $GMSPATH/gamess.$VERNO.x" >> $PROCFILE

 set path=(/opt/intel/impi/4.0.2.003/intel64/bin $path)

   setenv I_MPI_WAIT_MODE enable

   setenv I_MPI_PIN disable

   setenv I_MPI_DEBUG 0

   setenv I_MPI_STATS 0

   setenv I_MPI_DEVICE sock

   setenv I_MPI_NETMASK ib0

 setenv LD_LIBRARY_PATH /opt/intel/impi/4.0.2.003/intel64/lib:$LD_LIBRARY_PATH

 setenv LD_LIBRARY_PATH /opt/intel/composerxe-2011.4.191/compiler/lib/intel64:$LD_LIBRARY_PATH

 setenv LD_LIBRARY_PATH /opt/intel/composer_xe_2013.0.079/mkl/lib/intel64:$LD_LIBRARY_PATH

 setenv MKL_SERIAL YES

 setenv MKL_NUM_THREADS 1

 setenv LD_LIBRARY_PATH /usr/local/cuda/lib64:$LD_LIBRARY_PATH

 setenv GMS_CCHEM '1'

 @ NUMGPU=1

 setenv CCHEM 'devices=0;memory=4g'

 echo " * CPU cores:   `grep cores /proc/cpuinfo | wc -l` "

 echo " * GPU devices: $NUMGPU (with settings: $CCHEM)"

 echo " "

 chdir $SCR

 set echo

 mpdboot --rsh=ssh -n $NNODES -f $HOSTFILE

  mpiexec -configfile $PROCFILE < /dev/null

 mpdallexit

 unset echo

 rm -f $PROCFILE

endif

#----------------------------------------------------------------------

echo ----- accounting info -----

if ($GDDIjob == true) cp $SCR/$JOB.F07 ~/scr/$JOB.dat

echo Files used on the master node $master were:

ls -lF $SCR/$JOB.*

rm -f  $SCR/$JOB.F*

if (-e $SCR/$JOB.V84)        mv $SCR/$JOB.V84     $USERSCR

if (-e $SCR/$JOB.V80)        rm -f $SCR/$JOB.V*

if (-e $SCR/$JOB.TEMP02)     rm -f $SCR/$JOB.TEMP*

if (-e $SCR/$JOB.orb)        mv $SCR/$JOB.orb     $USERSCR

if (-e $SCR/$JOB.vec)        mv $SCR/$JOB.vec     $USERSCR

if (-e $SCR/$JOB.mol)        mv $SCR/$JOB.mol     $USERSCR

if (-e $SCR/$JOB.molf)       mv $SCR/$JOB.molf    $USERSCR

if (-e $SCR/$JOB.mkl)        mv $SCR/$JOB.mkl     $USERSCR

if (-e $SCR/$JOB.xyz)        mv $SCR/$JOB.xyz     $USERSCR

ls $SCR/${JOB}-*.cube > $SCR/${JOB}.lis

if (! -z $SCR/${JOB}.lis) mv $SCR/${JOB}*.cube $USERSCR

rm -f $SCR/${JOB}.lis

ls $SCR/${JOB}-*.grd > $SCR/${JOB}.lis

if (! -z $SCR/${JOB}.lis) mv $SCR/${JOB}*.grd $USERSCR

rm -f $SCR/${JOB}.lis

ls $SCR/${JOB}-*.csv > $SCR/${JOB}.lis

if (! -z $SCR/${JOB}.lis) mv $SCR/${JOB}*.csv $USERSCR

rm -f $SCR/${JOB}.lis

if ($TARGET == mpi) then

   set nnodes=`wc -l $HOSTFILE`

   set nnodes=$nnodes[1]

   @ n=1

   set master=`hostname`

   set master=$master:r

   while ($n <= $nnodes)

      set host=`sed -n -e "$n p" $HOSTFILE`

      set host=$host[1]

      if ($host != $master) then

         echo Files used on node $host were:

         ssh $host -l $USER "ls -l $SCR/$JOB.*"

         ssh $host -l $USER "rm -f $SCR/$JOB.*"

      endif

      @ n++

   end

   rm -f $HOSTFILE

   if ($?I_MPI_STATS) then

      if ($I_MPI_STATS > 0) mv $SCR/stats.txt ~/$JOB.$NCPUS.stats

   endif

endif

date

time

exit