Thank you Justin for your quick reply. Unfortunately I cannot use a more modern version of GROMACS as my topology and .gro files where first created for a reverse transformation from cg to fg and thus required the 3.3.1 version and some specific .itp files that are only present in that version. If I try to run it all with GORMACS 4.5 that it crashes immediately. I've also tried without the -cpo option but it doesn't change anything. I've checked the permission on the folder and as I supposed I have total access to it so it might not effect the results. If I open with vi a file with the same name as the .xtc file that I need for the script and write in it some crap just to try and then I just re run the mrdun command I don't get the error message anymore but gromacs complains saying Reading file dynamin_dimer_PR1.tpr, VERSION 3.3.1 (single precision) Loaded with Money
WARNING: Incomplete frame: nr 0 time 0 Segmentation fault I have checked with gmxcheck the .trr input file as it was suggested in another discussion, and apparently it is ok, so I really don't know what to do. Can you help me with that? Thanks Francesca Il giorno 31/gen/2012, alle ore 14.33, Justin A. Lemkul ha scritto: > > > Francesca Vitalini wrote: >> Actually the directory is of my own and I have created it in my home >> directory so that shouldn't be a problem as I also have created other files >> in the same directory without any problems so far. >> Other ideas? Thanks >> Francesca >> Il giorno 31/gen/2012, alle ore 13.02, Justin A. Lemkul ha scritto: >>> >>> francesca vitalini wrote: >>>> Hallo GROMACS users! >>>> 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 >>>> Reading file dynamin_dimer_PR1.tpr, VERSION 3.3.1 (single precision) >>>> Loaded with Money >>>> ------------------------------------------------------- >>>> Program mdrun, VERSION 3.3.1 >>>> Source code file: gmxfio.c, line: 706 >>>> Can not open file: >>>> coarse.xtc >>>> it is strange as the coarse.xtc file should be created by running the >>>> mdrun command. >>> Sounds to me like you don't have permission to write in the working >>> directory. >>> >>> -Justin >>> >>>> that is my submition command line >>>> $MYGROMACSPATH/bin/mdrun -v -s dynamin_dimer_PR1.tpr -o >>>> dynamin_dimer_PR1.trr -cpo dynamin_dimer_PR1.cpt -c dynamin_dimer_PR1.gro >>>> the .tpr file had been previously created by grompp > > I don't know if this is a problem or not, but I just noticed it. If you're > using version 3.3.1, the -cpo option doesn't exist. mdrun won't exit with a > fatal error in this case, but you still shouldn't be using it. > > Aside from that, I would suggest you use a more modern version of Gromacs > (4.5.5) rather than one that is certifiably ancient. There may well have > been some bug that was fixed 6 years ago that no one even remembers ;) > >>>> $MYGROMACSPATH/bin/grompp -v -f pr1.mdp -c dynamin_dimer_EM_solvated.gro >>>> -p dynamin_dimer_fg.top -o dynamin_dimer_PR1.tpr >>>> and the .mdp file I'm using is > > The .mdp file contains a number of redundancies, which should have caused > grompp to fail. Also probably irrelevant, but worth noting. > > -Justin > >>>> cpp = /lib/cpp >>>> constraints = all-bonds >>>> integrator = md >>>> tinit = 0.0 >>>> dt = 0.002 >>>> nsteps = 40000 >>>> nstcomm = 0 >>>> nstxout = 10000 >>>> nstvout = 10000 >>>> nstfout = 10000 >>>> nstlog = 10000 >>>> nstenergy = 100 >>>> nstxtcout = 100 >>>> xtc_precision = 1000 >>>> nstlist = 10 >>>> energygrps = Protein >>>> ns_type = grid >>>> rlist = 0.9 >>>> coulombtype = Generalized-Reaction-Field >>>> epsilon_rf = 62 >>>> rcoulomb = 1.5 >>>> rvdw = 1.0 >>>> ;Tcoupl = nose-hoover >>>> ;tc-grps = Protein >>>> ;ref_t = 300 >>>> nstxtcout = 100 >>>> xtc_precision = 1000 >>>> nstlist = 10 >>>> energygrps = Protein >>>> ns_type = grid >>>> rlist = 0.9 >>>> coulombtype = Generalized-Reaction-Field >>>> epsilon_rf = 62 >>>> rcoulomb = 1.5 >>>> rvdw = 1.0 >>>> ;Tcoupl = nose-hoover >>>> ;tc-grps = Protein >>>> ;ref_t = 300 >>>> ;tau_t = 0.1 >>>> ; Temperature coupling >>>> tcoupl = Berendsen ; Couple temperature to >>>> external heat bath according to Berendsen method >>>> tc-grps = Protein Non-Protein ; Use separate heat baths >>>> for Protein and Non-Protein groups >>>> tau_t = 0.1 0.1 ; Coupling time constant, >>>> controlling strength of coupling >>>> ref_t = 200 200 ; Temperature of heat bat >>>> I have also tried to change the .mdp file but I get the same error message. >>>> If I try to use a mdrun from a different version of GROMACS it complains >>>> again as it is not the same as grompp. >>>> Do you have any tips for solving this problem? >>>> Thanks >>>> Francesca >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the www interface >>> or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. 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