Hallo GROMACS users!<br>I'm trying to run a simple md script after running an energy minimization script on my system and I'm getting a wired error message<br><br>Reading file dynamin_dimer_PR1.tpr, VERSION 3.3.1 (single precision)<br>
Loaded with Money<br><br>-------------------------------------------------------<br>Program mdrun, VERSION 3.3.1<br>Source code file: gmxfio.c, line: 706<br><br>Can not open file:<br>coarse.xtc<br><br><br>it is strange as the coarse.xtc file should be created by running the mdrun command.<br>
<br>that is my submition command line<br><br>$MYGROMACSPATH/bin/mdrun -v -s dynamin_dimer_PR1.tpr -o dynamin_dimer_PR1.trr -cpo dynamin_dimer_PR1.cpt -c dynamin_dimer_PR1.gro<br><br>the .tpr file had been previously created by grompp<br>
<br>$MYGROMACSPATH/bin/grompp -v -f pr1.mdp -c dynamin_dimer_EM_solvated.gro -p dynamin_dimer_fg.top -o dynamin_dimer_PR1.tpr<br><br>and the .mdp file I'm using is<br><br>cpp = /lib/cpp<br>constraints = all-bonds<br>
integrator = md<br>tinit = 0.0<br>dt = 0.002<br>nsteps = 40000<br>nstcomm = 0<br>nstxout = 10000<br>nstvout = 10000<br>nstfout = 10000<br>
nstlog = 10000<br>nstenergy = 100<br>nstxtcout = 100<br>xtc_precision = 1000<br>nstlist = 10<br>energygrps = Protein<br>ns_type = grid<br>rlist = 0.9<br>
coulombtype = Generalized-Reaction-Field<br>epsilon_rf = 62<br>rcoulomb = 1.5<br>rvdw = 1.0<br><br>;Tcoupl = nose-hoover<br>;tc-grps = Protein<br>;ref_t = 300<br>
<br>nstxtcout = 100<br>xtc_precision = 1000<br>nstlist = 10<br>energygrps = Protein<br>ns_type = grid<br>rlist = 0.9<br>coulombtype = Generalized-Reaction-Field<br>
epsilon_rf = 62<br>rcoulomb = 1.5<br>rvdw = 1.0<br><br>;Tcoupl = nose-hoover<br>;tc-grps = Protein<br>;ref_t = 300<br>;tau_t = 0.1<br>
<br>; Temperature coupling<br>tcoupl = Berendsen ; Couple temperature to external heat bath according to Berendsen method<br>tc-grps = Protein Non-Protein ; Use separate heat baths for Protein and Non-Protein groups<br>
tau_t = 0.1 0.1 ; Coupling time constant, controlling strength of coupling<br>ref_t = 200 200 ; Temperature of heat bat<br><br>I have also tried to change the .mdp file but I get the same error message. <br>
If I try to use a mdrun from a different version of GROMACS it complains again as it is not the same as grompp.<br><br>Do you have any tips for solving this problem?<br><br>Thanks<br><br>Francesca<br>