[gmx-users] mdrun on GROMACS 3.3.1
Justin A. Lemkul
jalemkul at vt.edu
Tue Jan 31 17:22:00 CET 2012
francesca vitalini wrote:
> Well I'm keeping struggling with this script. Apparently the problem in
> in using the integrator md with the GOMACS 3.3.1 version. In fact the
> same .mdp file with integrator steep works. while with md it always
> gives the error message that it cannot open the .xtc file.
The md integrator can produce an .xtc file, steepest descent EM does not.
> How can I get around this problem?
> I can only see two ways now:
> -either there is a way to use md with GROMACS 3.3.1
> -or there is a way so that the mdrun of a newer version of GROMACS can
> deal with the file. If I try, even specifying the path for each .itp
> file, then the program cannot find certain atomtypes, such as
> Atomtype CH2R not found
> any suggestions here?
Some renaming has occurred for some atomtypes, and the force fields have been
re-organized in a more sensible fashion in newer versions. For instance, the
CH2R atom type in the Gromos96 force fields is now called CH2r.
-Justin
> Thanks
> Francesca
>
>
>
> 2012/1/31 Francesca Vitalini <francesca.vitalini11 at gmail.com
> <mailto:francesca.vitalini11 at gmail.com>>
>
> 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 <http://vt.edu> | (540) 231-9080
> <tel:%28540%29%20231-9080>
> >>> 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 <http://vt.edu> | (540) 231-9080
> <tel:%28540%29%20231-9080>
> > 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
========================================
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