[gmx-users] problem in equilibration step

[nitu sharma]

Dear all,

                     I am doing simulation of membrane protein for this I am
following justin's tutorial  In the first equilibration step i am getting
error like this-
-------------------------------------------------------
Program mdrun, VERSION 4.0.3
Source code file: trnio.c, line: 252

File input/output error:
Cannot write trajectory frame; maybe you are out of quota?

Can anyone have idea to solve this problem? If have please let me know.

My command line like this-

mdrun -v -s nvt.tpr -o new_seq-nvt.trr -c new_seq-nvt.gro -e
newe_seq-nvt.edr -g new_seq-nvt.log.

My nvt.mdp file is below-

title           = NVT equilibration for TAP-DMPC
define          = -DPOSRES      ; position restrain the protein
; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 25000         ; 2 * 25000 = 50 ps
dt              = 0.002         ; 2 fs
; Output control
nstxout         = 100           ; save coordinates every 0.2 ps
nstvout         = 100           ; save velocities every 0.2 ps
nstenergy       = 100           ; save energies every 0.2 ps
nstlog          = 100           ; update log file every 0.2 ps
; Bond parameters
continuation    = no            ; first dynamics run
constraint_algorithm = lincs    ; holonomic constraints
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
constrai
ned
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
ns_type         = grid          ; search neighboring grid cels
nstlist         = 5             ; 10 fs
rlist           = 1             ; short-range neighborlist cutoff (in nm)
rcoulomb        = 1             ; short-range electrostatic cutoff (in nm)
rvdw            = 1.2           ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype     = cut-off       ; coulombtype cut-off
pme_order       = 4             ; cubic interpolation
fourierspacing  = 0.16          ; grid spacing for FFT
; Temperature coupling is on
tcoupl          = V-rescale     ; modified Berendsen thermostat
tc-grps         = Protein DMPC SOL_NA+  ; three coupling groups - more
accurat
e
tau_t           = 0.1   0.1     0.1     ; time constant, in ps
ref_t           = 323   323     323     ; reference temperature, one for
each
group, in K
; Pressure coupling is off
pcoupl          = no            ; no pressure coupling in NVT
; Periodic boundary conditions
pbc             = xyz           ; 3-D PBC
; Dispersion correction
DispCorr        = EnerPres      ; account for cut-off vdW scheme
; Velocity generation
gen_vel         = yes           ; assign velocities from Maxwell
distribution
gen_temp        = 323           ; temperature for Maxwell distribution
gen_seed        = -1            ; generate a random seed

Thanks a lot in advance.

Nitu sharma
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090603/b40c92ba/attachment.html>