[gmx-users] restart

wnoid at hec.utah.edu wnoid at hec.utah.edu
Fri Feb 10 16:38:04 CET 2006

hello all.

first of all, many thanks to mr. yang ye for his help with my earlier
question.  (although, i am still curious to know exactly what grompp was

i have a question very closely related to yujie's and somewhat related to
mr. mark abraham's comments.  i am trying to ensure the continuity of
restarts of 4cpu bilayer simulations.  i have written a very simple script
to check this on our local cluster of 64 bit amd opteron
processors.  i compiled gromacs-3.3 in single precision on this cluster
using gnu compilers and i find that continuing ten 1 step simulations with
tpbconv agree with one 10 step simulation to within 1 part in 1e7.

however on a cluster of 32 bit intel xeon cpus my test fails very badly. 
on this cluster i compiled gromacs-3.3 in double precision using an intel
compiler.  when i compare two 1 step simulations (continued with tpbconv)
with one 2 step simulation i find that there are differences as large as 1
part in 1e3 in the trr files, even though the starting tpr files for both
sets of simulations are identical to within 1 part in 1e7.  from the trr
files i find that after one step there are differences in the forces and
after two steps differences show up even in the gro file output.  i am not
using temperature or pressure coupling and am updating the neighbor list
every step.

i start both simulations with grompp according to:
      $grompp -f $gr_inp -c $config -p $topol\
        -shuffle -np $nnodes\
        -o $gr_out -po $gr_sum -deshuf $gr_des >& $gr_log

i extend the 1 step simulation using tpbconv according to:
      $tpbconv -s $oldtpr -f $oldtrr -e $oldedr -extend $DeltaT\
         -o $newtpr >& $tpblog

my grompp input file for the 1 step simulation is the following:
(the input for the 2 step simulation is identical except nsteps =  2)

title               =  two 1step test
cpp                 =  /lib/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.001
tinit               =  0.0
nsteps              =  1
nstcomm             =  1
nstxout             =  1
nstvout             =  1
nstxtcout           = 1
xtc_precision       = 1000
nstfout             =  1
nstlog              =  1
nstenergy           =  1
nstlist             =  1
ns_type             =  grid
coulombtype         = pme
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.8
fourierspacing      = 0.08
pme_order           = 6
ewald_rtol          = 1.E-5
optimize_fft        = yes
Tcoupl              =  no
Pcoupl              =  no
gen_temp            =  308.0
gen_seed            =  48123
pbc = xyz

thanks to anyone who took the time to look at this.  any help would be
greatly appreciated.


will noid

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