[gmx-users] mdrun on GROMACS 3.3.1

[Justin A. Lemkul]

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
>>
>> ========================================
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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

========================================