time.pl

#!/usr/bin/perl

use strict;

my $iterations=shift;
my $groFile=shift;


open (TIMEFILE,">allTimes.txt") or die "schlupp";
close (TIMEFILE);

for (my $i=0;$i<$iterations;$i++){
        print "in schleife";
        #my $currentIts=100+1*$i;
        my $currentIts=$i;
        open (WRITEFILE, ">$currentIts.mdp") or die "Heureka, we died!";
        print WRITEFILE "title= PBSA minimization in vacuum\ncpp=/usr/bin/cpp\ndefine = -DFLEXIBLE -DPOSRES\nimplicit_solvent = GBSA\nintegrator = steep\nemtol = 1.0\nnsteps = $currentIts\nnstenergy = 1\nenergygrps = System\nns_type = grid\ncoulombtype = cut-off\nrcoulomb = 1.0\nrvdw = 1.0\nconstraints = none\npbc = no";
        close WRITEFILE;
        `/opt/SS12-Practical/gromacs/bin/grompp -v -f $currentIts.mdp -c 2gjxA_secondD_amber03_forgrompp.gro -p 2gjxA_secondD_amber03.top -o scwrl_WT_$currentIts.tpr`;
        open(TIMEFILE,">>allTimes.txt")or die "Huch wasn jetz hier so nech?";
        print TIMEFILE "$currentIts\t";
        close (TIMEFILE);
        `/usr/bin/time -o allTimes.txt -f "%E\treal\t%U\tuser\t%S\tsystem" -a /opt/SS12-Practical/gromacs/bin/mdrun -v -deffnm scwrl_WT_$currentIts.tpr > testnew.txt`;
        `rm mdout.mdp