[gmx-users] mdrun on GROMACS 3.3.1

[Justin A. Lemkul]

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
> 

-- 
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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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