[gmx-users] mdrun on GROMACS 3.3.1

[Francesca Vitalini]

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
>> $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
>> 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
> 
> ========================================
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