[gmx-users] INFLATEGRO SHRINKING SCRIPT ERROR

[Yogesh Sharma]

hello everyone,

I have been struggling with the automated script for shrinking iteration in
Professor lemkul tutorials. can anyone spot what am I doing wrong here?

















































































































* sh run_inflategro.sh                  ....Command line:  gmx grompp -f
minim_inflategro.mdp -c system_inflated.gro -p topol.top -r
system_inflated.gro -o system_inflated_em.tprNOTE 1 [file
minim_inflategro.mdp]:  With Verlet lists the optimal nstlist is >= 10,
with GPUs >= 20. Note  that with the Verlet scheme, nstlist has no effect
on the accuracy of  your simulation.Setting the LD random seed to
2088656998Generated 1038 of the 3486 non-bonded parameter
combinationsExcluding 3 bonded neighbours molecule type 'Protein'Excluding
3 bonded neighbours molecule type 'POPE'Excluding 3 bonded neighbours
molecule type 'U1NL'NOTE 2 [file topol.top, line 16988]:  System has
non-zero total charge: 3.999998  Total charge should normally be an
integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
<http://www.gromacs.org/Documentation/Floating_Point_Arithmetic>  for
discussion on how close it should be to an integer.  Removing all charge
groups because cutoff-scheme=VerletAnalysing residue names:There are:   271
   Protein residuesThere are:   333      Other residuesAnalysing
Protein...Analysing residues not classified as Protein/DNA/RNA/Water and
splitting into groups...Number of degrees of freedom in T-Coupling group
rest is 59709.00NOTE 3 [file minim_inflategro.mdp]:  You are using a plain
Coulomb cut-off, which might produce artifacts.  You might want to consider
using PME electrostatics.Command line:  gmx mdrun -deffnm
system_inflated_emReading file system_inflated_em.tpr, VERSION 5.1.2
(single precision)Using 1 MPI threadUsing 12 OpenMP threads Steepest
Descents:   Tolerance (Fmax)   =  1.00000e+03   Number of steps    =
 50000Energy minimization has stopped, but the forces have not converged to
therequested precision Fmax < 1000 (which may not be possible for your
system).It stopped because the algorithm tried to make a new step whose
size was toosmall, or there was no change in the energy since last step.
Either way, weregard the minimization as converged to within the available
machineprecision, given your starting configuration and EM
parameters.Double precision normally gives you higher accuracy, but this is
often notneeded for preparing to run molecular dynamics.writing lowest
energy coordinates.Steepest Descents converged to machine precision in 174
steps,but did not reach the requested Fmax < 1000.Potential Energy  =
-9.3649824e+07Maximum force     =  1.9553424e+14 on atom 17983Norm of force
    =  1.9600521e+12NOTE: 11 % of the run time was spent in pair search,
  you might want to increase nstlist (this has no effect on
accuracy)Command line:  gmx trjconv -s system_inflated_em.tpr -f
system_inflated_em.gro -o tmp.gro -pbc molWill write gro: Coordinate file
in Gromos-87 formatReading file system_inflated_em.tpr, VERSION 5.1.2
(single precision)Reading file system_inflated_em.tpr, VERSION 5.1.2
(single precision)Select group for outputGroup     0 (         System) has
19904 elementsGroup     1 (        Protein) has  2588 elementsGroup     2 (
     Protein-H) has  2034 elementsGroup     3 (        C-alpha) has   271
elementsGroup     4 (       Backbone) has   813 elementsGroup     5 (
 MainChain) has  1085 elementsGroup     6 (   MainChain+Cb) has  1332
elementsGroup     7 (    MainChain+H) has  1343 elementsGroup     8 (
 SideChain) has  1245 elementsGroup     9 (    SideChain-H) has   949
elementsGroup    10 (    Prot-Masses) has  2588 elementsGroup    11 (
 non-Protein) has 17316 elementsGroup    12 (          Other) has 17316
elementsGroup    13 (           POPE) has 17316 elementsSelect a group:
Selected 0: 'System'Reading frames from gro file 'U1NL', 19904
atoms.Reading frame       0 time    0.000   Precision of
system_inflated_em.gro is 0.001 (nm)Using output precision of 0.001
(nm)Last frame          0 time    0.000   gcq#339: "Look at these, my
work-strong arms" (P.J. Harvey)##########################################
RUNNING SHRINKING ITERATION
{1..26}...#########################################run_inflategro.sh: 33:
run_inflategro.sh: Illegal number: {1..26}*

if I have to do it manually without script, should this be the order of
commands including minimization?

perl inflategropl system_inflated_em.gro 0.95 POPE 0
system_shrink1.gro 5 area_shrink1.dat
gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top
-r system_inflated.gro -o system_inflated_em.tpr

gmx mdrun -deffnm system_inflated_em

gmx trjconv -s system_inflated_em.tpr -f system_inflated_em.gro -o
tmp.gro -pbc mol
mv tmp.gro system_inflated_em.gro

perl inflategropl system_inflated_em.gro 0.95 POPE 0
system_shrink1.gro 5 area_shrink1.dat...

...x 26