[gmx-users] mdrun on GROMACS 3.3.1
Francesca Vitalini
francesca.vitalini11 at gmail.com
Tue Jan 31 14:48:35 CET 2012
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
>>>
>>> ========================================
>>> --
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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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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