[gmx-users] mdrun on GROMACS 3.3.1
francesca vitalini
francesca.vitalini11 at gmail.com
Wed Feb 22 11:53:57 CET 2012
Hi,
sorry I'm back to this thread after quite a long time, as I was trying
to solve other problems. Now I'm back to the reverse transformation
tutorial on the martini webpage and whenever I try to use the mdp
script provided there for the annealing I just end up with the same
error message, which is that it cannot open the .xtc file that it is
supposed to create.
Program mdrun, VERSION 3.3.1
Source code file: gmxfio.c, line: 706
Can not open file:
annealing_LLL_frag.xtc
-------------------------------------------------------
"Love is Like Moby Dick, Get Chewed and Get Spat Out" (Urban Dance Squad)
Halting program mdrun
gcq#83: "Love is Like Moby Dick, Get Chewed and Get Spat Out" (Urban
Dance Squad)
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode -1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
The mdp file looks like
cpp = /lib/cpp
constraints = none
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 Water
ns_type = grid
rlist = 0.9
coulombtype = Generalized-Reaction-Field
epsilon_rf = 62
rcoulomb = 1
rvdw = 1.0
Tcoupl = nose-hoover
tc-grps = Protein Water
ref_t = 300 300
tau_t = 0.1 0.1
Pcoupl = no
table_extension = 1.2
;dihre = simple ; Some dihedrals are restrained for
instance peptide bonds are set to trans conformation.
;dihre_fc = 500
;dihre_tau = 0.0
;nstdihreout = 50
cap_force = 15000
cap_a = 100
fc_restr = 12000
r_CGW = 0.21
fc_restrW = 400
rel_steps = 0
rel_water = no
andersen_seed = 815131
annealing = single single
annealing_npoints = 2 2
annealing_time = 0 60 0 60 ; CHANGE HERE -annealing control
points for each group
annealing_temp = 1300 300 400 300 ; list of temperatures at
control points for each group
gen_vel = yes
gen_temp = 1300
gen_seed = 473529
lincs_warnangle = 100
Compared to the file of the tutorial I just have changed the number of
groups (2 instead of 3) and the rest is as the one that is provided,
so I really don't understand why is GROMACS 3.3.1 complaining.
Can you help me on that?
Thanks a lot
2012/1/31 Justin A. Lemkul <jalemkul at vt.edu>:
>
>
> 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
>> >>>
>> >>> ========================================
>> >>> --
>> >>> gmx-users mailing list gmx-users at gromacs.org
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>>
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>>
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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
>> >
>> > ========================================
>> > --
>> > gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>>
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>
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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
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