Hallo GROMACS users!<br>I&#39;m trying to run a simple md script after running an energy minimization script on my system and I&#39;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&#39;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>