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